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mfu_flist_io.c
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mfu_flist_io.c
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/* Implements functions to read/write an flist from/to a file */
#define _GNU_SOURCE
#include <dirent.h>
#include <fcntl.h>
#include <sys/syscall.h>
#include <limits.h>
#include <stdio.h>
#include <stdint.h>
#include <stdlib.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <string.h>
#include <unistd.h>
#include <getopt.h>
#include <time.h> /* asctime / localtime */
#include <regex.h>
#include <pwd.h> /* for getpwent */
#include <grp.h> /* for getgrent */
#include <errno.h>
#include <string.h>
#include "dtcmp.h"
#include "mfu.h"
#include "mfu_flist_internal.h"
/* variables to query for MPI error string */
static int mpierrlen;
static char mpierrstr[MPI_MAX_ERROR_STRING];
/* we try to use external32 when supported, since this format is standard
* across MPI libraries, we'll fall back to native */
static char datarep_ext32[] = "external32";
static char datarep_native[] = "native";
static void mfu_pack_io_uint32(char** pptr, uint32_t value)
{
/* convert from host to network order */
uint32_t* ptr = *(uint32_t**)pptr;
*ptr = mfu_hton32(value);
*pptr += 4;
}
static void mfu_unpack_io_uint32(const char** pptr, uint32_t* value)
{
/* convert from network to host order */
const uint32_t* ptr = *(const uint32_t**)pptr;
*value = mfu_ntoh32(*ptr);
*pptr += 4;
}
static void mfu_pack_io_uint64(char** pptr, uint64_t value)
{
/* convert from host to network order */
uint64_t* ptr = *(uint64_t**)pptr;
*ptr = mfu_hton64(value);
*pptr += 8;
}
static void mfu_unpack_io_uint64(const char** pptr, uint64_t* value)
{
/* convert from network to host order */
const uint64_t* ptr = *(const uint64_t**)pptr;
*value = mfu_ntoh64(*ptr);
*pptr += 8;
}
static size_t buft_pack_size(const buf_t* items)
{
size_t elem_size = items->chars + sizeof(uint64_t);
size_t pack_size = items->count * elem_size;
return pack_size;
}
static void buft_pack(void* buf, const buf_t* items)
{
char* dptr = (char*)buf;
const char* sptr = (const char*)items->buf;
uint64_t i;
for (i = 0; i < items->count; i++) {
/* copy path from source to destination buffer */
strncpy(dptr, sptr, items->chars);
sptr += items->chars;
dptr += items->chars;
/* pack uint64 into destination */
mfu_pack_io_uint64(&dptr, *(const uint64_t*)sptr);
sptr += sizeof(uint64_t);
}
return;
}
static void buft_unpack(const void* buf, buf_t* items)
{
const char* buf_ptr = (const char*)buf;
char* buft_ptr = (char*)items->buf;
uint64_t i;
for (i = 0; i < items->count; i++) {
/* copy path from buffer to buft */
strncpy(buft_ptr, buf_ptr, items->chars);
buft_ptr += items->chars;
buf_ptr += items->chars;
/* pack uint64 from buf into buft */
mfu_unpack_io_uint64(&buf_ptr, (uint64_t*)buft_ptr);
buft_ptr += sizeof(uint64_t);
}
return;
}
/* create a datatype to hold file name and stat info */
static void create_stattype(int detail, int chars, MPI_Datatype* dt_stat)
{
/* build type for file path */
MPI_Datatype dt_filepath;
MPI_Type_contiguous(chars, MPI_CHAR, &dt_filepath);
/* build keysat type */
int fields;
MPI_Datatype types[11];
if (detail) {
fields = 11;
types[0] = dt_filepath; /* file name */
types[1] = MPI_UINT64_T; /* mode */
types[2] = MPI_UINT64_T; /* uid */
types[3] = MPI_UINT64_T; /* gid */
types[4] = MPI_UINT64_T; /* atime secs */
types[5] = MPI_UINT64_T; /* atime nsecs */
types[6] = MPI_UINT64_T; /* mtime secs */
types[7] = MPI_UINT64_T; /* mtime nsecs */
types[8] = MPI_UINT64_T; /* ctime secs */
types[9] = MPI_UINT64_T; /* ctime nsecs */
types[10] = MPI_UINT64_T; /* size */
}
else {
fields = 2;
types[0] = dt_filepath; /* file name */
types[1] = MPI_UINT32_T; /* file type */
}
DTCMP_Type_create_series(fields, types, dt_stat);
MPI_Type_free(&dt_filepath);
return;
}
static size_t list_elem_encode_size(const elem_t* elem)
{
size_t reclen = strlen(elem->file); /* filename */
reclen += 2; /* | + type letter */
reclen += 1; /* trailing newline */
return reclen;
}
static size_t list_elem_encode(void* buf, const elem_t* elem)
{
char* ptr = (char*) buf;
size_t len = strlen(elem->file);
strncpy(ptr, elem->file, len);
ptr += len;
*ptr = '|';
ptr++;
mfu_filetype type = elem->type;
if (type == MFU_TYPE_FILE) {
*ptr = 'F';
}
else if (type == MFU_TYPE_DIR) {
*ptr = 'D';
}
else if (type == MFU_TYPE_LINK) {
*ptr = 'L';
}
else {
*ptr = 'U';
}
ptr++;
*ptr = '\n';
size_t reclen = len + 3;
return reclen;
}
/* given a buffer, decode element and store values in elem */
static void list_elem_decode(char* buf, elem_t* elem)
{
/* get name and advance pointer */
const char* file = strtok(buf, "|");
/* copy path */
elem->file = MFU_STRDUP(file);
/* set depth */
elem->depth = mfu_flist_compute_depth(file);
elem->detail = 0;
const char* type = strtok(NULL, "|");
if (type == NULL) {
elem->type = MFU_TYPE_UNKNOWN;
return;
}
char c = type[0];
if (c == 'F') {
elem->type = MFU_TYPE_FILE;
}
else if (c == 'D') {
elem->type = MFU_TYPE_DIR;
}
else if (c == 'L') {
elem->type = MFU_TYPE_LINK;
}
else {
elem->type = MFU_TYPE_UNKNOWN;
}
return;
}
/* create a datatype to hold file name and stat info */
/* return number of bytes needed to pack element */
static size_t list_elem_pack_size(int detail, uint64_t chars, const elem_t* elem)
{
size_t size;
if (detail) {
size = chars + 0 * 4 + 10 * 8;
}
else {
size = chars + 1 * 4;
}
return size;
}
/* pack element into buffer and return number of bytes written */
static size_t list_elem_pack(void* buf, int detail, uint64_t chars, const elem_t* elem)
{
/* set pointer to start of buffer */
char* start = (char*) buf;
char* ptr = start;
/* copy in file name */
char* file = elem->file;
strncpy(ptr, file, chars);
ptr += chars;
if (detail) {
mfu_pack_io_uint64(&ptr, elem->mode);
mfu_pack_io_uint64(&ptr, elem->uid);
mfu_pack_io_uint64(&ptr, elem->gid);
mfu_pack_io_uint64(&ptr, elem->atime);
mfu_pack_io_uint64(&ptr, elem->atime_nsec);
mfu_pack_io_uint64(&ptr, elem->mtime);
mfu_pack_io_uint64(&ptr, elem->mtime_nsec);
mfu_pack_io_uint64(&ptr, elem->ctime);
mfu_pack_io_uint64(&ptr, elem->ctime_nsec);
mfu_pack_io_uint64(&ptr, elem->size);
}
else {
/* just have the file type */
mfu_pack_io_uint32(&ptr, elem->type);
}
size_t bytes = (size_t)(ptr - start);
return bytes;
}
/* unpack element from buffer and return number of bytes read */
static size_t list_elem_unpack(const void* buf, int detail, uint64_t chars, elem_t* elem)
{
const char* start = (const char*) buf;
const char* ptr = start;
/* get name and advance pointer */
const char* file = ptr;
ptr += chars;
/* copy path */
elem->file = MFU_STRDUP(file);
/* set depth */
elem->depth = mfu_flist_compute_depth(file);
elem->detail = detail;
if (detail) {
/* extract fields */
mfu_unpack_io_uint64(&ptr, &elem->mode);
mfu_unpack_io_uint64(&ptr, &elem->uid);
mfu_unpack_io_uint64(&ptr, &elem->gid);
mfu_unpack_io_uint64(&ptr, &elem->atime);
mfu_unpack_io_uint64(&ptr, &elem->atime_nsec);
mfu_unpack_io_uint64(&ptr, &elem->mtime);
mfu_unpack_io_uint64(&ptr, &elem->mtime_nsec);
mfu_unpack_io_uint64(&ptr, &elem->ctime);
mfu_unpack_io_uint64(&ptr, &elem->ctime_nsec);
mfu_unpack_io_uint64(&ptr, &elem->size);
/* use mode to set file type */
elem->type = mfu_flist_mode_to_filetype((mode_t)elem->mode);
}
else {
mfu_unpack_io_uint32(&ptr, &elem->type);
}
size_t bytes = (size_t)(ptr - start);
return bytes;
}
/* insert a file given a pointer to packed data */
static void list_insert_decode(flist_t* flist, char* buf)
{
/* create new element to record file path, file type, and stat info */
elem_t* elem = (elem_t*) MFU_MALLOC(sizeof(elem_t));
/* decode buffer and store values in element */
list_elem_decode(buf, elem);
/* append element to tail of linked list */
mfu_flist_insert_elem(flist, elem);
return;
}
/* insert a file given a pointer to packed data */
static size_t list_insert_ptr(flist_t* flist, char* ptr, int detail, uint64_t chars)
{
/* create new element to record file path, file type, and stat info */
elem_t* elem = (elem_t*) MFU_MALLOC(sizeof(elem_t));
/* get name and advance pointer */
size_t bytes = list_elem_unpack(ptr, detail, chars, elem);
/* append element to tail of linked list */
mfu_flist_insert_elem(flist, elem);
return bytes;
}
/****************************************
* Read file list from file
***************************************/
static uint64_t get_filesize(const char* name)
{
uint64_t size = 0;
struct stat sb;
int rc = mfu_lstat(name, &sb);
if (rc == 0) {
size = (uint64_t) sb.st_size;
}
return size;
}
/* reads a file assuming variable length records stored one per line,
* data encoded in ASCII, fields separated by '|' characters,
* we divide the file into sections and each process is responsible
* for records in its section, tricky part is to handle records
* that spill from one section into the next */
static void read_cache_variable(
const char* name,
MPI_File fh,
const char* datarep,
flist_t* flist)
{
MPI_Status status;
/* get our rank and number of ranks in job */
int rank, ranks;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &ranks);
/* assume data records start at byte 0,
* need to update this code if this is not the case */
MPI_Offset disp = 0;
/* indicate that we just have file names */
flist->detail = 0;
/* get file size to determine how much each process should read,
* just have rank 0 read this and bcast to everyone */
uint64_t filesize;
if (rank == 0) {
filesize = get_filesize(name);
}
MPI_Bcast(&filesize, 1, MPI_UINT64_T, 0, MPI_COMM_WORLD);
/* TODO: consider stripe width */
/* compute number of chunks in file */
uint64_t chunk_size = 1024 * 1024;
uint64_t chunks = filesize / chunk_size;
if (chunks * chunk_size < filesize) {
chunks++;
}
/* compute chunk count for each process */
uint64_t chunk_count = chunks / (uint64_t) ranks;
uint64_t remainder = chunks - chunk_count * (uint64_t) ranks;
if ((uint64_t) rank < remainder) {
chunk_count++;
}
/* get our chunk offset */
uint64_t chunk_offset;
MPI_Exscan(&chunk_count, &chunk_offset, 1, MPI_UINT64_T, MPI_SUM, MPI_COMM_WORLD);
if (rank == 0) {
chunk_offset = 0;
}
/* in order to avoid blowing out memory, we read into a fixed-size
* buffer and unpack */
/* allocate a buffer, ensure it's large enough to hold at least one
* complete record */
size_t bufsize = chunk_size;
void* buf1 = MFU_MALLOC(bufsize);
void* buf2 = MFU_MALLOC(bufsize);
void* buf = buf1;
/* set file view to be sequence of characters past header */
int mpirc = MPI_File_set_view(fh, disp, MPI_CHAR, MPI_CHAR, datarep, MPI_INFO_NULL);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_LOG(MFU_LOG_ERR, "Failed to set view on file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
/* compute offset of first byte we'll read,
* the set_view above means we should start our offset at 0 */
MPI_Offset read_offset = (MPI_Offset)(chunk_offset * chunk_size);
/* compute offset of last byte we need to read,
* note we may actually read further if our last record spills
* into next chunk */
uint64_t last_offset = (uint64_t) disp + (chunk_offset + chunk_count) * chunk_size;
if (last_offset > filesize) {
last_offset = filesize;
}
/* read last character from chunk before our first,
* if this char is not a newline, then last record in the
* previous chunk spills into ours, in which case we need
* to scan past first newline */
/* assume we don't have to scan past first newline */
int scan = 0;
if (read_offset > 0) {
/* read last byte in chunk before our first */
MPI_Offset pos = read_offset - 1;
mpirc = MPI_File_read_at(fh, pos, buf, 1, MPI_CHAR, &status);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_LOG(MFU_LOG_ERR, "Failed to read file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
/* if last character is not newline, we need to scan past
* first new line in our chunk */
char* ptr = (char*) buf;
if (*ptr != '\n') {
scan = 1;
}
}
/* read data from file in chunks, decode records and insert in list */
uint64_t bufoffset = 0; /* offset within buffer where we should read data */
int done = 0;
while (! done) {
/* we're done if we there's nothing to read */
if ((uint64_t) read_offset >= filesize) {
break;
}
/* determine number to read, try to read a full buffer's worth,
* but reduce this if that overruns the end of the file */
int read_count = (int)(bufsize - bufoffset);
uint64_t remaining = filesize - (uint64_t) read_offset;
if (remaining < (uint64_t) read_count) {
read_count = (int) remaining;
}
/* read in our chunk */
char* bufstart = (char*) buf + bufoffset;
mpirc = MPI_File_read_at(fh, read_offset, bufstart, read_count, MPI_CHAR, &status);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_LOG(MFU_LOG_ERR, "Failed to read file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
/* TODO: check number of items read in status, in case file
* size changed somehow since we first read the file size */
/* update read offset for next time */
read_offset += (MPI_Offset) read_count;
/* setup pointers to work with read buffer,
* note that end points one char past last valid character */
char* ptr = (char*) buf;
char* end = ptr + bufoffset + read_count;
/* scan past first newline (first part of block is a partial
* record handled by another process) */
if (scan) {
/* advance to the next newline character */
while (ptr != end && *ptr != '\n') {
ptr++;
}
/* go one past newline character */
if (ptr != end) {
ptr++;
}
/* no need to do that again */
scan = 0;
}
/* process records */
char* start = ptr;
while (start != end) {
/* start points to beginning of a record, scan to
* search for end of record, advance ptr past next
* newline character or to end of buffer */
while (ptr != end && *ptr != '\n') {
ptr++;
}
/* process record if we hit a newline,
* otherwise copy partial record to other buffer */
if (ptr != end) {
/* we must be on a newline,
* terminate record string with NUL */
*ptr = '\0';
/* process record */
list_insert_decode(flist, start);
/* go one past newline character */
ptr++;
start = ptr;
/* compute position of last byte we read,
* stop if we have reached or exceeded the limit that
* need to read */
uint64_t pos = ((uint64_t)(read_offset - read_count)) - bufoffset + (uint64_t)(ptr - (char*)buf);
if (pos >= last_offset) {
done = 1;
break;
}
/* if newline was at end of buffer, reset offset into read buffer */
if (ptr >= end) {
bufoffset = 0;
}
}
else {
/* hit end of buffer but not end of record,
* copy partial record to start of next buffer */
/* swap buffers */
if (buf == buf1) {
buf = buf2;
}
else {
buf = buf1;
}
/* copy remainder to next buffer */
size_t len = (size_t)(ptr - start);
memcpy(buf, start, len);
bufoffset = (uint64_t) len;
/* done with this buffer */
break;
}
}
}
/* free buffer */
mfu_free(&buf2);
mfu_free(&buf1);
buf = NULL;
return;
}
/* file format:
* uint64_t timestamp when walk started
* uint64_t timestamp when walk ended
* uint64_t total number of users
* uint64_t max username length
* uint64_t total number of groups
* uint64_t max groupname length
* uint64_t total number of files
* uint64_t max filename length
* list of <username(str), userid(uint64_t)>
* list of <groupname(str), groupid(uint64_t)>
* list of <files(str)>
* */
static void read_cache_v3(
const char* name,
MPI_Offset* outdisp,
MPI_File fh,
const char* datarep,
uint64_t* outstart,
uint64_t* outend,
flist_t* flist)
{
MPI_Status status;
MPI_Offset disp = *outdisp;
/* indicate that we have stat data */
flist->detail = 1;
/* pointer to users, groups, and file buffer data structure */
buf_t* users = &flist->users;
buf_t* groups = &flist->groups;
/* get our rank */
int rank, ranks;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &ranks);
/* rank 0 reads and broadcasts header */
uint64_t header[8];
int mpirc = MPI_File_set_view(fh, disp, MPI_UINT64_T, MPI_UINT64_T, datarep, MPI_INFO_NULL);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_ABORT(1, "Failed to set view on file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
if (rank == 0) {
mpirc = MPI_File_read_at(fh, 0, header, 8, MPI_UINT64_T, &status);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_ABORT(1, "Failed to read file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
}
MPI_Bcast(header, 8, MPI_UINT64_T, 0, MPI_COMM_WORLD);
disp += 8 * 8; /* 8 consecutive uint64_t types in external32 */
uint64_t all_count;
*outstart = header[0];
*outend = header[1];
users->count = header[2];
users->chars = header[3];
groups->count = header[4];
groups->chars = header[5];
all_count = header[6];
uint64_t chars = header[7];
/* compute count for each process */
uint64_t count = all_count / (uint64_t)ranks;
uint64_t remainder = all_count - count * (uint64_t)ranks;
if ((uint64_t)rank < remainder) {
count++;
}
/* get our offset */
uint64_t offset;
MPI_Exscan(&count, &offset, 1, MPI_UINT64_T, MPI_SUM, MPI_COMM_WORLD);
if (rank == 0) {
offset = 0;
}
/* read users, if any */
if (users->count > 0 && users->chars > 0) {
/* create type */
mfu_flist_usrgrp_create_stridtype((int)users->chars, &(users->dt));
/* get extent */
MPI_Aint lb_user, extent_user;
MPI_Type_get_extent(users->dt, &lb_user, &extent_user);
/* allocate memory to hold data */
size_t bufsize_user = users->count * (size_t)extent_user;
users->buf = (void*) MFU_MALLOC(bufsize_user);
users->bufsize = bufsize_user;
/* read data */
mpirc = MPI_File_set_view(fh, disp, users->dt, users->dt, datarep, MPI_INFO_NULL);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_LOG(MFU_LOG_ERR, "Failed to set view on file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
if (rank == 0) {
mpirc = MPI_File_read_at(fh, 0, users->buf, (int)users->count, users->dt, &status);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_LOG(MFU_LOG_ERR, "Failed to read file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
}
MPI_Bcast(users->buf, (int)users->count, users->dt, 0, MPI_COMM_WORLD);
disp += (MPI_Offset) bufsize_user;
}
/* read groups, if any */
if (groups->count > 0 && groups->chars > 0) {
/* create type */
mfu_flist_usrgrp_create_stridtype((int)groups->chars, &(groups->dt));
/* get extent */
MPI_Aint lb_group, extent_group;
MPI_Type_get_extent(groups->dt, &lb_group, &extent_group);
/* allocate memory to hold data */
size_t bufsize_group = groups->count * (size_t)extent_group;
groups->buf = (void*) MFU_MALLOC(bufsize_group);
groups->bufsize = bufsize_group;
/* read data */
mpirc = MPI_File_set_view(fh, disp, groups->dt, groups->dt, datarep, MPI_INFO_NULL);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_LOG(MFU_LOG_ERR, "Failed to set view on file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
if (rank == 0) {
mpirc = MPI_File_read_at(fh, 0, groups->buf, (int)groups->count, groups->dt, &status);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_LOG(MFU_LOG_ERR, "Failed to read file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
}
MPI_Bcast(groups->buf, (int)groups->count, groups->dt, 0, MPI_COMM_WORLD);
disp += (MPI_Offset) bufsize_group;
}
/* read files, if any */
if (all_count > 0 && chars > 0) {
/* create types */
MPI_Datatype dt;
create_stattype(flist->detail, (int)chars, &dt);
/* get extents */
MPI_Aint lb_file, extent_file;
MPI_Type_get_extent(dt, &lb_file, &extent_file);
/* in order to avoid blowing out memory, we'll pack into a smaller
* buffer and iteratively make many collective reads */
/* allocate a buffer, ensure it's large enough to hold at least one
* complete record */
size_t bufsize = 1024 * 1024;
if (bufsize < (size_t) extent_file) {
bufsize = (size_t) extent_file;
}
void* buf = MFU_MALLOC(bufsize);
/* compute number of items we can fit in each read iteration */
uint64_t bufcount = (uint64_t)bufsize / (uint64_t)extent_file;
/* determine number of iterations we need to read all items */
uint64_t iters = count / bufcount;
if (iters * bufcount < count) {
iters++;
}
/* compute max iterations across all procs */
uint64_t all_iters;
MPI_Allreduce(&iters, &all_iters, 1, MPI_UINT64_T, MPI_MAX, MPI_COMM_WORLD);
/* set file view to be sequence of datatypes past header */
mpirc = MPI_File_set_view(fh, disp, dt, dt, datarep, MPI_INFO_NULL);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_LOG(MFU_LOG_ERR, "Failed to set view on file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
/* compute byte offset to read our element */
MPI_Offset read_offset = (MPI_Offset)offset;
/* iterate with multiple reads until all records are read */
uint64_t totalcount = 0;
while (all_iters > 0) {
/* determine number to read */
int read_count = (int) bufcount;
uint64_t remaining = count - totalcount;
if (remaining < bufcount) {
read_count = (int) remaining;
}
/* TODO: read_at_all w/ external32 is broken in ROMIO as of MPICH-3.2rc1 */
/* issue a collective read */
//MPI_File_read_at_all(fh, read_offset, buf, read_count, dt, &status);
mpirc = MPI_File_read_at(fh, read_offset, buf, read_count, dt, &status);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_LOG(MFU_LOG_ERR, "Failed to read file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
/* update our offset with the number of items we just read */
read_offset += (MPI_Offset)read_count;
totalcount += (uint64_t) read_count;
/* unpack data from buffer into list */
char* ptr = (char*) buf;
uint64_t packcount = 0;
while (packcount < (uint64_t) read_count) {
/* unpack item from buffer and advance pointer */
list_insert_ptr(flist, ptr, 1, chars);
ptr += extent_file;
packcount++;
}
/* one less iteration */
all_iters--;
}
/* free buffer */
mfu_free(&buf);
/* free off our datatype */
MPI_Type_free(&dt);
}
/* create maps of users and groups */
mfu_flist_usrgrp_create_map(&flist->users, flist->user_id2name);
mfu_flist_usrgrp_create_map(&flist->groups, flist->group_id2name);
*outdisp = disp;
return;
}
/* file format:
* all integer values stored in network byte order
*
* uint64_t file version
* uint64_t total number of users
* uint64_t max username length
* uint64_t total number of groups
* uint64_t max groupname length
* uint64_t total number of files
* uint64_t max filename length
* list of <username(str), userid(uint64_t)>
* list of <groupname(str), groupid(uint64_t)>
* list of <files(str)>
* */
static void read_cache_v4(
const char* name,
MPI_Offset* outdisp,
MPI_File fh,
const char* datarep,
flist_t* flist)
{
MPI_Status status;
MPI_Offset disp = *outdisp;
/* indicate that we have stat data */
flist->detail = 1;
/* pointer to users, groups, and file buffer data structure */
buf_t* users = &flist->users;
buf_t* groups = &flist->groups;
/* get our rank */
int rank, ranks;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &ranks);
/* rank 0 reads and broadcasts header */
uint64_t header[6];
int header_size = 6 * 8; /* 6 consecutive uint64_t */
int mpirc = MPI_File_set_view(fh, disp, MPI_BYTE, MPI_BYTE, datarep, MPI_INFO_NULL);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_ABORT(1, "Failed to set view on file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
if (rank == 0) {
uint64_t header_packed[6];
mpirc = MPI_File_read_at(fh, 0, header_packed, header_size, MPI_BYTE, &status);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_ABORT(1, "Failed to read file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
const char* ptr = (const char*) header_packed;
mfu_unpack_io_uint64(&ptr, &header[0]);
mfu_unpack_io_uint64(&ptr, &header[1]);
mfu_unpack_io_uint64(&ptr, &header[2]);
mfu_unpack_io_uint64(&ptr, &header[3]);
mfu_unpack_io_uint64(&ptr, &header[4]);
mfu_unpack_io_uint64(&ptr, &header[5]);
}
MPI_Bcast(header, 6, MPI_UINT64_T, 0, MPI_COMM_WORLD);
disp += header_size;
uint64_t all_count;
users->count = header[0];
users->chars = header[1];
groups->count = header[2];
groups->chars = header[3];
all_count = header[4];
uint64_t chars = header[5];
/* compute count for each process */
uint64_t count = all_count / (uint64_t)ranks;
uint64_t remainder = all_count - count * (uint64_t)ranks;
if ((uint64_t)rank < remainder) {
count++;
}
/* get our offset */
uint64_t offset;
MPI_Exscan(&count, &offset, 1, MPI_UINT64_T, MPI_SUM, MPI_COMM_WORLD);
if (rank == 0) {
offset = 0;
}
/* read users, if any */
if (users->count > 0 && users->chars > 0) {
/* create type */
mfu_flist_usrgrp_create_stridtype((int)users->chars, &(users->dt));
/* get extent */
MPI_Aint lb_user, extent_user;
MPI_Type_get_extent(users->dt, &lb_user, &extent_user);
/* allocate memory to hold data */
size_t bufsize_user = users->count * (size_t)extent_user;
users->buf = (void*) MFU_MALLOC(bufsize_user);
users->bufsize = bufsize_user;
/* set view to read data */
mpirc = MPI_File_set_view(fh, disp, MPI_BYTE, MPI_BYTE, datarep, MPI_INFO_NULL);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_ABORT(1, "Failed to set view on file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
/* read data */
int user_buf_size = (int) buft_pack_size(users);
if (rank == 0) {
char* user_buf = (char*) MFU_MALLOC(user_buf_size);
mpirc = MPI_File_read_at(fh, 0, user_buf, user_buf_size, MPI_BYTE, &status);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_ABORT(1, "Failed to read file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
buft_unpack(user_buf, users);
mfu_free(&user_buf);
}
MPI_Bcast(users->buf, (int)users->count, users->dt, 0, MPI_COMM_WORLD);
disp += (MPI_Offset) user_buf_size;
}
/* read groups, if any */
if (groups->count > 0 && groups->chars > 0) {
/* create type */
mfu_flist_usrgrp_create_stridtype((int)groups->chars, &(groups->dt));
/* get extent */
MPI_Aint lb_group, extent_group;
MPI_Type_get_extent(groups->dt, &lb_group, &extent_group);
/* allocate memory to hold data */
size_t bufsize_group = groups->count * (size_t)extent_group;
groups->buf = (void*) MFU_MALLOC(bufsize_group);
groups->bufsize = bufsize_group;
/* set view to read data */
mpirc = MPI_File_set_view(fh, disp, MPI_BYTE, MPI_BYTE, datarep, MPI_INFO_NULL);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_ABORT(1, "Failed to set view on file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
/* read data */
int group_buf_size = (int) buft_pack_size(groups);
if (rank == 0) {
char* group_buf = (char*) MFU_MALLOC(group_buf_size);
mpirc = MPI_File_read_at(fh, 0, group_buf, group_buf_size, MPI_BYTE, &status);
if (mpirc != MPI_SUCCESS) {
MPI_Error_string(mpirc, mpierrstr, &mpierrlen);
MFU_ABORT(1, "Failed to read file: `%s' rc=%d %s", name, mpirc, mpierrstr);
}
buft_unpack(group_buf, groups);
mfu_free(&group_buf);
}
MPI_Bcast(groups->buf, (int)groups->count, groups->dt, 0, MPI_COMM_WORLD);
disp += (MPI_Offset) group_buf_size;
}
/* read files, if any */
if (all_count > 0 && chars > 0) {
/* get size of file element */
size_t elem_size = list_elem_pack_size(flist->detail, (int)chars, NULL);
/* in order to avoid blowing out memory, we'll pack into a smaller
* buffer and iteratively make many collective reads */
/* allocate a buffer, ensure it's large enough to hold at least one
* complete record */