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io.c
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io.c
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#include "hdf5.h"
#include "mpi.h"
#include "pca.h"
#include <stdio.h>
#include <math.h>
// assumes matInfo was preallocated
double getMatrixInfo(char * infilename, char * datasetname, MPI_Comm *comm, MPI_Info *info, distMatrixInfo *matInfo) {
double startTime = MPI_Wtime();
int mpi_size, mpi_rank;
MPI_Comm_size(*comm, &mpi_size);
MPI_Comm_rank(*comm, &mpi_rank);
hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(plist_id, *comm, *info);
hid_t file_id = H5Fopen(infilename, H5F_ACC_RDONLY, plist_id);
if (file_id < 0) {
fprintf(stderr, "Error opening %s\n", infilename);
exit(-1);
}
hid_t dataset_id = H5Dopen(file_id, datasetname, H5P_DEFAULT);
if (dataset_id < 0) {
fprintf(stderr, "Error opening %s in %s : are you sure this dataset exists?\n", datasetname, infilename);
exit(-1);
}
hid_t dataset_space = H5Dget_space(dataset_id);
hsize_t dims[2];
herr_t status = H5Sget_simple_extent_dims(dataset_space, dims, NULL);
if (status < 0 || status != 2) {
fprintf(stderr, "Error reading %s from %s : remember it should be a 2d matrix\n", datasetname, infilename);
exit(-1);
}
H5Sclose(dataset_space);
H5Dclose(dataset_id);
H5Fclose(file_id);
H5Pclose(plist_id);
int numrows = dims[0];
int numcols = dims[1];
int littlePartitionSize = numrows/mpi_size;
int bigPartitionSize = littlePartitionSize + 1;
int numLittlePartitions = mpi_size - numrows % mpi_size;
int numBigPartitions = numrows % mpi_size;
int localrows, startingrow;
if (mpi_rank < numBigPartitions) {
localrows = bigPartitionSize;
startingrow = bigPartitionSize*mpi_rank;
} else {
localrows = littlePartitionSize;
startingrow = bigPartitionSize*numBigPartitions +
littlePartitionSize*(mpi_rank - numBigPartitions);
}
matInfo->mpi_size = mpi_size;
matInfo->mpi_rank = mpi_rank;
matInfo->numrows = numrows;
matInfo->numcols = numcols;
matInfo->localrows = localrows;
matInfo->startingrow = startingrow;
matInfo->littlePartitionSize = littlePartitionSize;
matInfo->bigPartitionSize = bigPartitionSize;
matInfo->numLittlePartitions = numLittlePartitions;
matInfo->numBigPartitions = numBigPartitions;
matInfo->comm = comm;
matInfo->rowcounts = (int *) malloc ( mpi_size * sizeof(int) );
matInfo->rowoffsets = (int *) malloc ( mpi_size * sizeof(int) );
if (matInfo->rowcounts == NULL || matInfo->rowoffsets == NULL) {
fprintf(stderr, "Could not allocate memory for the matrix chunk offset information\n");
exit(-1);
}
for(int idx = 0; idx < numBigPartitions; idx = idx + 1) {
matInfo->rowcounts[idx] = bigPartitionSize;
matInfo->rowoffsets[idx] = bigPartitionSize * idx;
}
for(int idx = numBigPartitions; idx < mpi_size; idx = idx + 1) {
matInfo->rowcounts[idx] = littlePartitionSize;
matInfo->rowoffsets[idx] = bigPartitionSize * numBigPartitions + littlePartitionSize * (idx - numBigPartitions);
}
return MPI_Wtime() - startTime;
}
void freeMatrixInfo(distMatrixInfo * matInfo) {
free(matInfo->rowcounts);
free(matInfo->rowoffsets);
}
double genGatherInfo(distMatrixInfo *matInfo, int numeigs, distGatherInfo *eigInfo) {
double startTime = MPI_Wtime();
int mpi_size = matInfo->mpi_size;
int bigPartitionSize = matInfo->bigPartitionSize;
int numBigPartitions = matInfo->numBigPartitions;
int littlePartitionSize = matInfo->littlePartitionSize;
int numLittlePartitions = matInfo->numLittlePartitions;
eigInfo->elementcounts = (int *) malloc( mpi_size * sizeof(int));
eigInfo->elementoffsets = (int *) malloc( mpi_size * sizeof(int));
eigInfo->rowcounts = (int *) malloc( mpi_size * sizeof(int));
eigInfo->rowoffsets = (int *) malloc( mpi_size * sizeof(int));
if (eigInfo->elementcounts == NULL || eigInfo->elementoffsets == NULL
|| eigInfo->rowcounts == NULL || eigInfo->rowoffsets == NULL) {
fprintf(stderr, "Couldn't allocate memory for the eigenvector matrix information\n");
exit(-1);
}
for(int idx = 0; idx < numBigPartitions; idx = idx + 1) {
eigInfo->elementcounts[idx] = bigPartitionSize * numeigs;
eigInfo->elementoffsets[idx] = bigPartitionSize * numeigs * idx;
eigInfo->rowcounts[idx] = bigPartitionSize;
eigInfo->rowoffsets[idx] = bigPartitionSize * idx;
}
for(int idx = numBigPartitions; idx < mpi_size; idx = idx + 1) {
eigInfo->elementcounts[idx] = littlePartitionSize * numeigs;
eigInfo->elementoffsets[idx] = bigPartitionSize * numeigs * numBigPartitions +
littlePartitionSize * numeigs * (idx - numBigPartitions);
eigInfo->rowcounts[idx] = littlePartitionSize;
eigInfo->rowoffsets[idx] = bigPartitionSize * numBigPartitions + littlePartitionSize * (idx - numBigPartitions);
}
eigInfo->numrows = matInfo->numrows;
eigInfo->numcols = matInfo->numcols;
eigInfo->numeigs = numeigs;
return MPI_Wtime() - startTime;
}
void freeGatherInfo(distGatherInfo *eigInfo) {
free(eigInfo->elementcounts);
free(eigInfo->elementoffsets);
free(eigInfo->rowcounts);
free(eigInfo->rowoffsets);
}
// localRowChunk will be allocated inside the function
double loadMatrix(char * infilename, char * datasetname, distMatrixInfo
*matInfo, double ** localRowChunk, MPI_Comm *comm, MPI_Info *info) {
double startTime = MPI_Wtime();
// assuming double inputs, check that the chunks aren't too big to be read
// by HDF5 in parallel mode
if (matInfo->bigPartitionSize*matInfo->numcols >= 268435456 &&
matInfo->mpi_rank == 0) {
fprintf(stderr, "MPIIO-based HDF5 is limited to reading 2GiB at most in "
"each call to read; try increasing the number of processors\n");
exit(-1); }
*localRowChunk = (double *) malloc( matInfo->localrows * matInfo->numcols *sizeof(double) );
if (*localRowChunk == NULL) {
fprintf(stderr, "Could not allocate enough memory for the local chunk "
"of rows for %s in process %d\n", datasetname, matInfo->mpi_rank);
exit(-1);
}
hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(plist_id, *comm, *info);
hid_t file_id = H5Fopen(infilename, H5F_ACC_RDONLY, plist_id);
if (file_id < 0) {
fprintf(stderr, "Error opening %s\n", infilename);
exit(-1);
}
hid_t dataset_id = H5Dopen(file_id, datasetname, H5P_DEFAULT);
if (dataset_id < 0) {
fprintf(stderr, "Error opening %s in %s : are you sure this dataset "
"exists?\n", datasetname, infilename);
exit(-1);
}
hsize_t offset[2], count[2], offset_out[2];
count[0] = matInfo->localrows;
count[1] = matInfo->numcols;
offset[0] = matInfo->mpi_rank < matInfo->numBigPartitions ?
(matInfo->mpi_rank * matInfo->bigPartitionSize) :
(matInfo->numBigPartitions * matInfo->bigPartitionSize +
(matInfo->mpi_rank - matInfo->numBigPartitions) *
matInfo->littlePartitionSize );
offset[1] = 0;
hid_t filespace = H5Dget_space(dataset_id);
if ( H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) {
fprintf(stderr, "Error selecting input file hyperslab in process %d\n",
matInfo->mpi_rank);
exit(-1);
}
hid_t memspace = H5Screate_simple(2, count, NULL);
offset_out[0] = 0;
offset_out[1] = 0;
if ( H5Sselect_hyperslab(memspace, H5S_SELECT_SET, offset_out, NULL, count, NULL) < 0 ) {
fprintf(stderr, "Error selecting memory hyperslab in process %d\n",
matInfo->mpi_rank);
exit(-1);
}
hid_t daccess_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(daccess_id, H5FD_MPIO_INDEPENDENT); // collective io seems slow for this
if (matInfo->mpi_rank == 0) {
printf("Loading matrix from dataset %s in file %s\n", datasetname,
infilename);
}
if( H5Dread(dataset_id, H5T_NATIVE_DOUBLE, memspace, filespace, daccess_id, *localRowChunk) < 0) {
fprintf(stderr, "Error reading dataset in process %d\n", matInfo->mpi_rank);
exit(-1);
}
H5Pclose(daccess_id);
H5Sclose(memspace);
H5Sclose(filespace);
H5Dclose(dataset_id);
H5Fclose(file_id);
H5Pclose(plist_id);
return MPI_Wtime() - startTime;
}
// loads the latitudes of each row from the given file, and returns the corresponding vector of row weights in rowWeights
// expects each line of the file to be in the form ^idx,latitude$
// returns sqrt(cos(lat)) as the weights vector; should be called only by one process
double loadRowWeights(char * weightsFname, double * rowWeights) {
int rowIdx;
double latVal;
double loadTime = MPI_Wtime();
printf("Loading latitudes for each observation from file %s\n", weightsFname);
FILE * fin = fopen(weightsFname, "r");
if( fin == NULL ) {
fprintf(stderr, "Can't open latitude csv file %s!\n", weightsFname);
exit(1);
}
while(fscanf(fin, "%d,%lf", &rowIdx, &latVal) != EOF) {
rowWeights[rowIdx] = sqrt(cos(latVal*M_PI/180.0));
}
fclose(fin);
return MPI_Wtime() - loadTime;
}
void writeSVD(char * outfname, distGatherInfo *eigInfo, double * U, double * V, double * singvals, double * meanVec, double * rowWeights) {
hid_t file_id = H5Fcreate(outfname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if (file_id < 0) {
fprintf(stderr, "Could not create output file %s\n", outfname);
exit(-1);
}
hsize_t dims[2];
dims[0] = eigInfo->numrows;
dims[1] = eigInfo->numeigs;
hid_t dataspace_id = H5Screate_simple(2, dims, NULL);
hid_t dataset_id = H5Dcreate2(file_id, "/U", H5T_NATIVE_DOUBLE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
hid_t plist_id = H5Pcreate(H5P_DATASET_XFER);
if (dataset_id < 0) {
fprintf(stderr, "Error creating dataset U in %s\n", outfname);
exit(-1);
}
if( H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, dataspace_id, plist_id, U) < 0) {
fprintf(stderr, "Error writing U to %s\n", outfname);
exit(-1);
}
H5Dclose(dataset_id);
H5Sclose(dataspace_id);
dims[0] = eigInfo->numcols;
dims[1] = eigInfo->numeigs;
dataspace_id = H5Screate_simple(2, dims, NULL);
dataset_id = H5Dcreate2(file_id, "/V", H5T_NATIVE_DOUBLE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (dataset_id < 0) {
fprintf(stderr, "Error creating dataset V in %s\n", outfname);
exit(-1);
}
if ( H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, dataspace_id, plist_id, V) < 0 ) {
fprintf(stderr, "Error writing V to %s\n", outfname);
exit(-1);
}
H5Dclose(dataset_id);
H5Sclose(dataspace_id);
dims[0] = eigInfo->numeigs;
dataspace_id = H5Screate_simple(1, dims, NULL);
dataset_id = H5Dcreate2(file_id, "/S", H5T_NATIVE_DOUBLE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (dataset_id < 0) {
fprintf(stderr, "Error creating dataset S in %s\n", outfname);
exit(-1);
}
if ( H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, dataspace_id, plist_id, singvals) < 0) {
fprintf(stderr, "Error writing S to %s\n", outfname);
exit(-1);
}
H5Dclose(dataset_id);
H5Sclose(dataspace_id);
dims[0] = eigInfo->numrows;
dataspace_id = H5Screate_simple(1, dims, NULL);
dataset_id = H5Dcreate2(file_id, "/rowMeans", H5T_NATIVE_DOUBLE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (dataset_id < 0) {
fprintf(stderr, "Error creating dataset rowMeans in %s\n", outfname);
exit(-1);
}
if ( H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, dataspace_id, plist_id, meanVec) < 0) {
fprintf(stderr, "Error writing rowMeans to %s\n", outfname);
exit(-1);
}
H5Dclose(dataset_id);
H5Sclose(dataspace_id);
dims[0] = eigInfo->numrows;
dataspace_id = H5Screate_simple(1, dims, NULL);
dataset_id = H5Dcreate2(file_id, "/rowWeights", H5T_NATIVE_DOUBLE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (dataset_id < 0) {
fprintf(stderr, "Error creating dataset rowWeights in %s\n", outfname);
exit(-1);
}
if ( H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, dataspace_id, plist_id, rowWeights) < 0) {
fprintf(stderr, "Error writing rowWeights to %s\n", outfname);
exit(-1);
}
H5Dclose(dataset_id);
H5Sclose(dataspace_id);
H5Pclose(plist_id);
H5Fclose(file_id);
}