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phastaIO.cc
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phastaIO.cc
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/*
*
* This is the SyncIO library that uses MPI-IO collective functions to
* implement a flexible I/O checkpoint solution for a large number of
* processors.
*
* Previous developer: Ning Liu ([email protected])
* Jing Fu ([email protected])
* Current developers: Michel Rasquin ([email protected]),
* Ben Matthews ([email protected])
*
*/
#include <map>
#include <vector>
#include <string>
#include <cstdarg>
#include <string.h>
#include <ctype.h>
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <sstream>
#include "phastaIO.h"
#include "phiotmrc.h"
#include "phiompi.h"
#include "mpi.h"
#include "phiostats.h"
#include "phiotimer.h"
#include <assert.h>
/* OS-specific things try to stay here */
#include <sys/stat.h>
#include <unistd.h>
#include <errno.h>
#define VERSION_INFO_HEADER_SIZE 8192
#define DB_HEADER_SIZE 1024
#define ONE_MEGABYTE 1048576
#define TWO_MEGABYTE 2097152
#define ENDIAN_TEST_NUMBER 12180 // Troy's Zip Code!!
#define MAX_PHASTA_FILES 64
#define MAX_PHASTA_FILE_NAME_LENGTH 1024
#define MAX_FIELDS_NUMBER ((VERSION_INFO_HEADER_SIZE/MAX_FIELDS_NAME_LENGTH)-4) // The meta data include - MPI_IO_Tag, nFields, nFields*names of the fields, nppf
// -3 for MPI_IO_Tag, nFields and nppf, -4 for extra security (former nFiles)
#define MAX_FIELDS_NAME_LENGTH 128
#define DefaultMHSize (4*ONE_MEGABYTE)
//#define DefaultMHSize (8350) //For test
#define LATEST_WRITE_VERSION 1
#define inv1024sq 953.674316406e-9 // = 1/1024/1024
int MasterHeaderSize = -1;
bool PRINT_PERF = false; // default print no perf results
int irank = -1; // global rank, should never be manually manipulated
int mysize = -1;
// Static variables are bad but used here to store the subcommunicator and associated variables
// Prevent MPI_Comm_split to be called more than once, especially on BGQ with the V1R2M1 driver (leak detected in MPI_Comm_split - IBM working on it)
static int s_assign_local_comm = 0;
static MPI_Comm s_local_comm;
static int s_local_size = -1;
static int s_local_rank = -1;
// the following defines are for debug printf
#define PHASTAIO_DEBUG 0 //default to not print any debugging info
void phprintf(const char* fmt, ...) {
(void)fmt;
#if PHASTAIO_DEBUG
char format[1024];
snprintf(format, sizeof(format), "phastaIO debug: %s", fmt);
va_list ap;
va_start(ap,fmt);
vprintf(format,ap);
va_end(ap);
#endif
}
void phprintf_0(const char* fmt, ...) {
(void)fmt;
#if PHASTAIO_DEBUG
int rank = 0;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
if(rank == 0){
char format[1024];
snprintf(format, sizeof(format), "phastaIO debug: irank=0 %s", fmt);
va_list ap;
va_start(ap,fmt);
vprintf(format, ap);
va_end(ap);
}
#endif
}
enum PhastaIO_Errors
{
MAX_PHASTA_FILES_EXCEEDED = -1,
UNABLE_TO_OPEN_FILE = -2,
NOT_A_MPI_FILE = -3,
GPID_EXCEEDED = -4,
DATA_TYPE_ILLEGAL = -5
};
using namespace std;
namespace{
map<int, std::string> LastHeaderKey;
vector< FILE* > fileArray;
vector< bool > byte_order;
vector< int > header_type;
int DataSize=0;
bool LastHeaderNotFound = false;
bool Wrong_Endian = false ;
bool Strict_Error = false ;
bool binary_format = true;
/***********************************************************************/
/***************** NEW PHASTA IO CODE STARTS HERE **********************/
/***********************************************************************/
typedef struct
{
char filename[MAX_PHASTA_FILE_NAME_LENGTH]; /* defafults to 1024 */
unsigned long my_offset;
unsigned long next_start_address;
unsigned long **my_offset_table;
unsigned long **my_read_table;
double * double_chunk;
double * read_double_chunk;
int field_count;
int part_count;
int read_field_count;
int read_part_count;
int GPid;
int start_id;
int mhsize;
int myrank;
int numprocs;
int local_myrank;
int local_numprocs;
int nppp;
int nPPF;
int nFiles;
int nFields;
int * int_chunk;
int * read_int_chunk;
int Wrong_Endian; /* default to false */
char * master_header;
MPI_File file_handle;
MPI_Comm local_comm;
} phastaio_file_t;
typedef struct
{
int nppf, nfields;
char * masterHeader;
}serial_file;
serial_file *SerialFile;
phastaio_file_t *PhastaIOActiveFiles[MAX_PHASTA_FILES];
int PhastaIONextActiveIndex = 0; /* indicates next index to allocate */
// the caller has the responsibility to delete the returned string
// TODO: StringStipper("nbc value? ") returns NULL?
char* StringStripper( const char istring[] ) {
int length = strlen( istring );
char* dest = (char *)malloc( length + 1 );
strcpy( dest, istring );
dest[ length ] = '\0';
if ( char* p = strpbrk( dest, " ") )
*p = '\0';
return dest;
}
inline int cscompare( const char teststring[], const char targetstring[] ) {
char* s1 = const_cast<char*>(teststring);
char* s2 = const_cast<char*>(targetstring);
while( *s1 == ' ') s1++;
while( *s2 == ' ') s2++;
while( ( *s1 )
&& ( *s2 )
&& ( *s2 != '?')
&& ( tolower( *s1 )==tolower( *s2 ) ) ) {
s1++;
s2++;
while( *s1 == ' ') s1++;
while( *s2 == ' ') s2++;
}
if ( !( *s1 ) || ( *s1 == '?') ) return 1;
else return 0;
}
inline void isBinary( const char iotype[] ) {
char* fname = StringStripper( iotype );
if ( cscompare( fname, "binary" ) ) binary_format = true;
else binary_format = false;
free (fname);
}
inline size_t typeSize( const char typestring[] ) {
char* ts1 = StringStripper( typestring );
if ( cscompare( "integer", ts1 ) ) {
free (ts1);
return sizeof(int);
} else if ( cscompare( "double", ts1 ) ) {
free (ts1);
return sizeof( double );
} else {
free (ts1);
fprintf(stderr,"unknown type : %s\n",ts1);
return 0;
}
}
int readHeader(
FILE* fileObject,
const char phrase[],
int* params,
int expect ) {
char* text_header;
char* token;
char Line[1024] = "\0";
char junk;
bool FOUND = false ;
int real_length;
int skip_size, integer_value;
int rewind_count=0;
if( !fgets( Line, 1024, fileObject ) && feof( fileObject ) ) {
rewind( fileObject );
clearerr( fileObject );
rewind_count++;
fgets( Line, 1024, fileObject );
}
while( !FOUND && ( rewind_count < 2 ) ) {
if ( ( Line[0] != '\n' ) && ( real_length = strcspn( Line, "#" )) ) {
text_header = (char *)malloc( real_length + 1 );
strncpy( text_header, Line, real_length );
text_header[ real_length ] =static_cast<char>(NULL);
token = strtok ( text_header, ":" );
assert(token);
if( cscompare( phrase , token ) ) {
FOUND = true ;
token = strtok( NULL, " ,;<>" );
assert(token);
skip_size = atoi( token );
int i;
for( i=0; i < expect && ( token = strtok( NULL," ,;<>") ); i++) {
assert(token);
params[i] = atoi( token );
}
if ( i < expect ) {
fprintf(stderr,
"Aloha Expected # of ints not found for: %s\n",phrase );
}
} else if ( cscompare(token,"byteorder magic number") ) {
if ( binary_format ) {
fread((void*)&integer_value,sizeof(int),1,fileObject);
fread( &junk, sizeof(char), 1 , fileObject );
if ( 362436 != integer_value ) Wrong_Endian = true;
} else{
fscanf(fileObject, "%d\n", &integer_value );
}
} else {
/* some other header, so just skip over */
token = strtok( NULL, " ,;<>" );
assert(token);
skip_size = atoi( token );
if ( binary_format)
fseek( fileObject, skip_size, SEEK_CUR );
else
for( int gama=0; gama < skip_size; gama++ )
fgets( Line, 1024, fileObject );
}
free (text_header);
} // end of if before while loop
if ( !FOUND )
if( !fgets( Line, 1024, fileObject ) && feof( fileObject ) ) {
rewind( fileObject );
clearerr( fileObject );
rewind_count++;
fgets( Line, 1024, fileObject );
}
}
if ( !FOUND ) {
//fprintf(stderr, "Error: Could not find: %s\n", phrase);
if(irank == 0) printf("WARNING: Could not find: %s\n", phrase);
return 1;
}
return 0;
}
} // end unnamed namespace
// begin of publicly visible functions
/**
* This function takes a long long pointer and assign (start) phiotmrc value to it
*/
void startTimer(double* start) {
if( !PRINT_PERF ) return;
MPI_Barrier(MPI_COMM_WORLD);
*start = phiotmrc();
}
/**
* This function takes a long long pointer and assign (end) phiotmrc value to it
*/
void endTimer(double* end) {
if( !PRINT_PERF ) return;
*end = phiotmrc();
MPI_Barrier(MPI_COMM_WORLD);
}
/**
* choose to print some performance results (or not) according to
* the PRINT_PERF macro
*/
void printPerf(
const char* func_name,
double start,
double end,
unsigned long datasize,
int printdatainfo,
const char* extra_msg) {
if( !PRINT_PERF ) return;
unsigned long data_size = datasize;
double time = end - start;
unsigned long isizemin,isizemax,isizetot;
double sizemin,sizemax,sizeavg,sizetot,rate;
double tmin, tmax, tavg, ttot;
MPI_Allreduce(&time, &tmin,1, MPI_DOUBLE, MPI_MIN, MPI_COMM_WORLD);
MPI_Allreduce(&time, &tmax,1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD);
MPI_Allreduce(&time, &ttot,1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
tavg = ttot/mysize;
if(irank == 0) {
if ( PhastaIONextActiveIndex == 0 ) printf("** 1PFPP ");
else printf("** syncIO ");
printf("%s(): Tmax = %f sec, Tmin = %f sec, Tavg = %f sec", func_name, tmax, tmin, tavg);
}
if(printdatainfo == 1) { // if printdatainfo ==1, compute I/O rate and block size
MPI_Allreduce(&data_size,&isizemin,1,MPI_LONG_LONG_INT,MPI_MIN,MPI_COMM_WORLD);
MPI_Allreduce(&data_size,&isizemax,1,MPI_LONG_LONG_INT,MPI_MAX,MPI_COMM_WORLD);
MPI_Allreduce(&data_size,&isizetot,1,MPI_LONG_LONG_INT,MPI_SUM,MPI_COMM_WORLD);
sizemin=(double)(isizemin*inv1024sq);
sizemax=(double)(isizemax*inv1024sq);
sizetot=(double)(isizetot*inv1024sq);
sizeavg=(double)(1.0*sizetot/mysize);
rate=(double)(1.0*sizetot/tmax);
if( irank == 0) {
printf(", Rate = %f MB/s [%s] \n \t\t\t"
" block size: Min= %f MB; Max= %f MB; Avg= %f MB; Tot= %f MB\n",
rate, extra_msg, sizemin,sizemax,sizeavg,sizetot);
}
}
else {
if(irank == 0) {
printf(" \n");
//printf(" (%s) \n", extra_msg);
}
}
}
/**
* This function is normally called at the beginning of a read operation, before
* init function.
* This function (uses rank 0) reads out nfields, nppf, master header size,
* endianess and allocates for masterHeader string.
* These values are essential for following read operations. Rank 0 will bcast
* these values to other ranks in the commm world
*
* If the file set is of old POSIX format, it would throw error and exit
*/
void queryphmpiio(const char filename[],int *nfields, int *nppf)
{
MPI_Comm_rank(MPI_COMM_WORLD, &irank);
MPI_Comm_size(MPI_COMM_WORLD, &mysize);
if(irank == 0) {
FILE * fileHandle;
char* fname = StringStripper( filename );
PHASTAIO_OPENTIME(fileHandle = fopen (fname,"rb");)
if (fileHandle == NULL ) {
printf("\nError: File %s doesn't exist! Please check!\n",fname);
}
else {
SerialFile =(serial_file *)calloc( 1, sizeof( serial_file) );
int meta_size_limit = VERSION_INFO_HEADER_SIZE;
SerialFile->masterHeader = (char *)malloc( meta_size_limit );
fread(SerialFile->masterHeader, 1, meta_size_limit, fileHandle);
char read_out_tag[MAX_FIELDS_NAME_LENGTH];
char version[MAX_FIELDS_NAME_LENGTH/4];
int mhsize;
char * token;
int magic_number;
memcpy( read_out_tag,
SerialFile->masterHeader,
MAX_FIELDS_NAME_LENGTH-1 );
if ( cscompare ("MPI_IO_Tag",read_out_tag) ) {
// Test endianess ...
memcpy (&magic_number,
SerialFile->masterHeader + sizeof("MPI_IO_Tag : ")-1, //-1 sizeof returns the size of the string+1 for "\0"
sizeof(int) ); // masterheader should look like "MPI_IO_Tag : 12180 " with 12180 in binary format
if ( magic_number != ENDIAN_TEST_NUMBER ) {
printf("Endian is different!\n");
// Will do swap later
}
// test version, old version, default masterheader size is 4M
// newer version masterheader size is read from first line
memcpy(version,
SerialFile->masterHeader + MAX_FIELDS_NAME_LENGTH/2,
MAX_FIELDS_NAME_LENGTH/4 - 1); //TODO: why -1?
if( cscompare ("version",version) ) {
// if there is "version" tag in the file, then it is newer format
// read master header size from here, otherwise use default
// Note: if version is "1", we know mhsize is at 3/4 place...
token = strtok(version, ":");
token = strtok(NULL, " ,;<>" );
int iversion = atoi(token);
if( iversion == 1) {
memcpy( &mhsize,
SerialFile->masterHeader + MAX_FIELDS_NAME_LENGTH/4*3 + sizeof("mhsize : ")-1,
sizeof(int));
if ( magic_number != ENDIAN_TEST_NUMBER )
SwapArrayByteOrder(&mhsize, sizeof(int), 1);
if( mhsize > DefaultMHSize ) {
//if actual headersize is larger than default, let's re-read
free(SerialFile->masterHeader);
SerialFile->masterHeader = (char *)malloc(mhsize);
fseek(fileHandle, 0, SEEK_SET); // reset the file stream position
fread(SerialFile->masterHeader,1,mhsize,fileHandle);
}
}
//TODO: check if this is a valid int??
MasterHeaderSize = mhsize;
}
else { // else it's version 0's format w/o version tag, implicating MHSize=4M
MasterHeaderSize = DefaultMHSize;
}
memcpy( read_out_tag,
SerialFile->masterHeader+MAX_FIELDS_NAME_LENGTH+1,
MAX_FIELDS_NAME_LENGTH ); //TODO: why +1
// Read in # fields ...
token = strtok( read_out_tag, ":" );
token = strtok( NULL," ,;<>" );
*nfields = atoi( token );
if ( *nfields > MAX_FIELDS_NUMBER) {
printf("Error queryphmpiio: nfields is larger than MAX_FIELDS_NUMBER!\n");
}
SerialFile->nfields=*nfields; //TODO: sanity check of this int?
memcpy( read_out_tag,
SerialFile->masterHeader + MAX_FIELDS_NAME_LENGTH * 2
+ *nfields * MAX_FIELDS_NAME_LENGTH,
MAX_FIELDS_NAME_LENGTH);
token = strtok( read_out_tag, ":" );
token = strtok( NULL," ,;<>" );
*nppf = atoi( token );
SerialFile->nppf=*nppf; //TODO: sanity check of int
} // end of if("MPI_IO_TAG")
else {
printf("Error queryphmpiio: The file you opened is not of syncIO new format, please check! read_out_tag = %s\n",read_out_tag);
exit(1);
}
PHASTAIO_CLOSETIME(fclose(fileHandle);)
free(SerialFile->masterHeader);
free(SerialFile);
} //end of else
free(fname);
}
// Bcast value to every one
MPI_Bcast( nfields, 1, MPI_INT, 0, MPI_COMM_WORLD );
MPI_Bcast( nppf, 1, MPI_INT, 0, MPI_COMM_WORLD );
MPI_Bcast( &MasterHeaderSize, 1, MPI_INT, 0, MPI_COMM_WORLD );
phprintf("Info queryphmpiio: myrank = %d, MasterHeaderSize = %d\n", irank, MasterHeaderSize);
}
/**
* This function computes the right master header size (round to size of 2^n).
* This is only needed for file format version 1 in "write" mode.
*/
int computeMHSize(int nfields, int nppf, int version) {
int mhsize=0;
if(version == 1) {
//int meta_info_size = (2+nfields+1) * MAX_FIELDS_NAME_LENGTH; // 2 is MPI_IO_TAG and nFields, the others 1 is nppf
int meta_info_size = VERSION_INFO_HEADER_SIZE;
int actual_size = nfields * nppf * sizeof(unsigned long) + meta_info_size;
//printf("actual_size = %d, offset table size = %d\n", actual_size, nfields * nppf * sizeof(long long));
if (actual_size > DefaultMHSize) {
mhsize = (int) ceil( (double) actual_size/DefaultMHSize); // it's rounded to ceiling of this value
mhsize *= DefaultMHSize;
}
else {
mhsize = DefaultMHSize;
}
} else {
int rank = 0;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
if(!rank) {
fprintf(stderr,
"ERROR invalid version passed to %s... exiting\n", __func__);
exit(EXIT_FAILURE);
}
}
return mhsize;
}
/**
* Computes correct color of a rank according to number of files.
*/
extern "C" int computeColor( int myrank, int numprocs, int nfiles) {
int color =
(int)(myrank / (numprocs / nfiles));
return color;
}
/**
* Check the file descriptor.
*/
void checkFileDescriptor(const char fctname[], int* fileDescriptor ) {
if ( *fileDescriptor < 0 ) {
printf("Error: File descriptor = %d in %s\n",*fileDescriptor,fctname);
exit(1);
}
}
/**
* Initialize the file struct members and allocate space for file struct
* buffers.
*
* Note: this function is only called when we are using new format. Old POSIX
* format should skip this routine and call openfile() directly instead.
*/
int initphmpiio( int *nfields, int *nppf, int *nfiles, int *filehandle, const char mode[])
{
// we init irank again in case query not called (e.g. syncIO write case)
MPI_Comm_rank(MPI_COMM_WORLD, &irank);
MPI_Comm_size(MPI_COMM_WORLD, &mysize);
phprintf("Info initphmpiio: entering function, myrank = %d, MasterHeaderSize = %d, nfields %d, nppf %d, nfiles %d\n", irank, MasterHeaderSize, *nfields, *nppf, *nfiles);
double timer_start, timer_end;
startTimer(&timer_start);
char* imode = StringStripper( mode );
// Note: if it's read, we presume query was called prior to init and
// MasterHeaderSize is already set to correct value from parsing header
// otherwise it's write then it needs some computation to be set
if ( cscompare( "read", imode ) ) {
// do nothing
}
else if( cscompare( "write", imode ) ) {
MasterHeaderSize = computeMHSize(*nfields, *nppf, LATEST_WRITE_VERSION);
}
else {
printf("Error initphmpiio: can't recognize the mode %s", imode);
exit(1);
}
free ( imode );
phprintf("Info initphmpiio: myrank = %d, MasterHeaderSize = %d\n", irank, MasterHeaderSize);
int i, j;
if( PhastaIONextActiveIndex == MAX_PHASTA_FILES ) {
printf("Error initphmpiio: PhastaIONextActiveIndex = MAX_PHASTA_FILES");
endTimer(&timer_end);
printPerf("initphmpiio", timer_start, timer_end, 0, 0, "");
return MAX_PHASTA_FILES_EXCEEDED;
}
// else if( PhastaIONextActiveIndex == 0 ) //Hang in debug mode on Intrepid
// {
// for( i = 0; i < MAX_PHASTA_FILES; i++ );
// {
// PhastaIOActiveFiles[i] = NULL;
// }
// }
PhastaIOActiveFiles[PhastaIONextActiveIndex] = (phastaio_file_t *)calloc( 1, sizeof( phastaio_file_t) );
i = PhastaIONextActiveIndex;
PhastaIONextActiveIndex++;
//PhastaIOActiveFiles[i]->next_start_address = 2*TWO_MEGABYTE;
PhastaIOActiveFiles[i]->next_start_address = MasterHeaderSize; // what does this mean??? TODO
PhastaIOActiveFiles[i]->Wrong_Endian = false;
PhastaIOActiveFiles[i]->nFields = *nfields;
PhastaIOActiveFiles[i]->nPPF = *nppf;
PhastaIOActiveFiles[i]->nFiles = *nfiles;
MPI_Comm_rank(MPI_COMM_WORLD, &(PhastaIOActiveFiles[i]->myrank));
MPI_Comm_size(MPI_COMM_WORLD, &(PhastaIOActiveFiles[i]->numprocs));
if( *nfiles > 1 ) { // split the ranks according to each mpiio file
if ( s_assign_local_comm == 0) { // call mpi_comm_split for the first (and only) time
if (PhastaIOActiveFiles[i]->myrank == 0) printf("Building subcommunicator\n");
int color = computeColor(PhastaIOActiveFiles[i]->myrank, PhastaIOActiveFiles[i]->numprocs, PhastaIOActiveFiles[i]->nFiles);
MPI_Comm_split(MPI_COMM_WORLD,
color,
PhastaIOActiveFiles[i]->myrank,
&(PhastaIOActiveFiles[i]->local_comm));
MPI_Comm_size(PhastaIOActiveFiles[i]->local_comm,
&(PhastaIOActiveFiles[i]->local_numprocs));
MPI_Comm_rank(PhastaIOActiveFiles[i]->local_comm,
&(PhastaIOActiveFiles[i]->local_myrank));
// back up now these variables so that we do not need to call comm_split again
s_local_comm = PhastaIOActiveFiles[i]->local_comm;
s_local_size = PhastaIOActiveFiles[i]->local_numprocs;
s_local_rank = PhastaIOActiveFiles[i]->local_myrank;
s_assign_local_comm = 1;
}
else { // recycle the subcommunicator
if (PhastaIOActiveFiles[i]->myrank == 0) printf("Recycling subcommunicator\n");
PhastaIOActiveFiles[i]->local_comm = s_local_comm;
PhastaIOActiveFiles[i]->local_numprocs = s_local_size;
PhastaIOActiveFiles[i]->local_myrank = s_local_rank;
}
}
else { // *nfiles == 1 here - no need to call mpi_comm_split here
if (PhastaIOActiveFiles[i]->myrank == 0) printf("Bypassing subcommunicator\n");
PhastaIOActiveFiles[i]->local_comm = MPI_COMM_WORLD;
PhastaIOActiveFiles[i]->local_numprocs = PhastaIOActiveFiles[i]->numprocs;
PhastaIOActiveFiles[i]->local_myrank = PhastaIOActiveFiles[i]->myrank;
}
PhastaIOActiveFiles[i]->nppp =
PhastaIOActiveFiles[i]->nPPF/PhastaIOActiveFiles[i]->local_numprocs;
PhastaIOActiveFiles[i]->start_id = PhastaIOActiveFiles[i]->nPPF *
(int)(PhastaIOActiveFiles[i]->myrank/PhastaIOActiveFiles[i]->local_numprocs) +
(PhastaIOActiveFiles[i]->local_myrank * PhastaIOActiveFiles[i]->nppp);
PhastaIOActiveFiles[i]->my_offset_table =
( unsigned long ** ) calloc( MAX_FIELDS_NUMBER , sizeof( unsigned long *) );
PhastaIOActiveFiles[i]->my_read_table =
( unsigned long ** ) calloc( MAX_FIELDS_NUMBER , sizeof( unsigned long *) );
for (j=0; j<*nfields; j++)
{
PhastaIOActiveFiles[i]->my_offset_table[j] =
( unsigned long * ) calloc( PhastaIOActiveFiles[i]->nppp , sizeof( unsigned long) );
PhastaIOActiveFiles[i]->my_read_table[j] =
( unsigned long * ) calloc( PhastaIOActiveFiles[i]->nppp , sizeof( unsigned long) );
}
*filehandle = i;
PhastaIOActiveFiles[i]->master_header = (char *)calloc(MasterHeaderSize,sizeof( char ));
PhastaIOActiveFiles[i]->double_chunk = (double *)calloc(1,sizeof( double ));
PhastaIOActiveFiles[i]->int_chunk = (int *)calloc(1,sizeof( int ));
PhastaIOActiveFiles[i]->read_double_chunk = (double *)calloc(1,sizeof( double ));
PhastaIOActiveFiles[i]->read_int_chunk = (int *)calloc(1,sizeof( int ));
// Time monitoring
endTimer(&timer_end);
printPerf("initphmpiio", timer_start, timer_end, 0, 0, "");
phprintf_0("Info initphmpiio: quiting function");
return i;
}
/**
* Destruct the file struct and free buffers allocated in init function.
*/
void finalizephmpiio( int *fileDescriptor )
{
double timer_start, timer_end;
startTimer(&timer_start);
int i, j;
i = *fileDescriptor;
//PhastaIONextActiveIndex--;
/* //free the offset table for this phasta file */
//for(j=0; j<MAX_FIELDS_NUMBER; j++) //Danger: undefined behavior for my_*_table.[j] not allocated or not initialized to NULL
for(j=0; j<PhastaIOActiveFiles[i]->nFields; j++)
{
free( PhastaIOActiveFiles[i]->my_offset_table[j]);
free( PhastaIOActiveFiles[i]->my_read_table[j]);
}
free ( PhastaIOActiveFiles[i]->my_offset_table );
free ( PhastaIOActiveFiles[i]->my_read_table );
free ( PhastaIOActiveFiles[i]->master_header );
free ( PhastaIOActiveFiles[i]->double_chunk );
free ( PhastaIOActiveFiles[i]->int_chunk );
free ( PhastaIOActiveFiles[i]->read_double_chunk );
free ( PhastaIOActiveFiles[i]->read_int_chunk );
if( PhastaIOActiveFiles[i]->nFiles > 1 && s_assign_local_comm ) { // the comm was split
if (PhastaIOActiveFiles[i]->myrank == 0) printf("Freeing subcommunicator\n");
s_assign_local_comm = 0;
MPI_Comm_free(&(PhastaIOActiveFiles[i]->local_comm));
}
free( PhastaIOActiveFiles[i]);
endTimer(&timer_end);
printPerf("finalizempiio", timer_start, timer_end, 0, 0, "");
PhastaIONextActiveIndex--;
}
/**
* Special init for M2N in order to create a subcommunicator for the reduced solution (requires PRINT_PERF to be false for now)
* Initialize the file struct members and allocate space for file struct buffers.
*
* Note: this function is only called when we are using new format. Old POSIX
* format should skip this routine and call openfile() directly instead.
*/
int initphmpiiosub( int *nfields, int *nppf, int *nfiles, int *filehandle, const char mode[],MPI_Comm my_local_comm)
{
// we init irank again in case query not called (e.g. syncIO write case)
MPI_Comm_rank(my_local_comm, &irank);
MPI_Comm_size(my_local_comm, &mysize);
phprintf("Info initphmpiio: entering function, myrank = %d, MasterHeaderSize = %d\n", irank, MasterHeaderSize);
double timer_start, timer_end;
startTimer(&timer_start);
char* imode = StringStripper( mode );
// Note: if it's read, we presume query was called prior to init and
// MasterHeaderSize is already set to correct value from parsing header
// otherwise it's write then it needs some computation to be set
if ( cscompare( "read", imode ) ) {
// do nothing
}
else if( cscompare( "write", imode ) ) {
MasterHeaderSize = computeMHSize(*nfields, *nppf, LATEST_WRITE_VERSION);
}
else {
printf("Error initphmpiio: can't recognize the mode %s", imode);
exit(1);
}
free ( imode );
phprintf("Info initphmpiio: myrank = %d, MasterHeaderSize = %d\n", irank, MasterHeaderSize);
int i, j;
if( PhastaIONextActiveIndex == MAX_PHASTA_FILES ) {
printf("Error initphmpiio: PhastaIONextActiveIndex = MAX_PHASTA_FILES");
endTimer(&timer_end);
printPerf("initphmpiio", timer_start, timer_end, 0, 0, "");
return MAX_PHASTA_FILES_EXCEEDED;
}
// else if( PhastaIONextActiveIndex == 0 ) //Hang in debug mode on Intrepid
// {
// for( i = 0; i < MAX_PHASTA_FILES; i++ );
// {
// PhastaIOActiveFiles[i] = NULL;
// }
// }
PhastaIOActiveFiles[PhastaIONextActiveIndex] = (phastaio_file_t *)calloc( 1, sizeof( phastaio_file_t) );
i = PhastaIONextActiveIndex;
PhastaIONextActiveIndex++;
//PhastaIOActiveFiles[i]->next_start_address = 2*TWO_MEGABYTE;
PhastaIOActiveFiles[i]->next_start_address = MasterHeaderSize; // what does this mean??? TODO
PhastaIOActiveFiles[i]->Wrong_Endian = false;
PhastaIOActiveFiles[i]->nFields = *nfields;
PhastaIOActiveFiles[i]->nPPF = *nppf;
PhastaIOActiveFiles[i]->nFiles = *nfiles;
MPI_Comm_rank(my_local_comm, &(PhastaIOActiveFiles[i]->myrank));
MPI_Comm_size(my_local_comm, &(PhastaIOActiveFiles[i]->numprocs));
int color = computeColor(PhastaIOActiveFiles[i]->myrank, PhastaIOActiveFiles[i]->numprocs, PhastaIOActiveFiles[i]->nFiles);
MPI_Comm_split(my_local_comm,
color,
PhastaIOActiveFiles[i]->myrank,
&(PhastaIOActiveFiles[i]->local_comm));
MPI_Comm_size(PhastaIOActiveFiles[i]->local_comm,
&(PhastaIOActiveFiles[i]->local_numprocs));
MPI_Comm_rank(PhastaIOActiveFiles[i]->local_comm,
&(PhastaIOActiveFiles[i]->local_myrank));
PhastaIOActiveFiles[i]->nppp =
PhastaIOActiveFiles[i]->nPPF/PhastaIOActiveFiles[i]->local_numprocs;
PhastaIOActiveFiles[i]->start_id = PhastaIOActiveFiles[i]->nPPF *
(int)(PhastaIOActiveFiles[i]->myrank/PhastaIOActiveFiles[i]->local_numprocs) +
(PhastaIOActiveFiles[i]->local_myrank * PhastaIOActiveFiles[i]->nppp);
PhastaIOActiveFiles[i]->my_offset_table =
( unsigned long ** ) calloc( MAX_FIELDS_NUMBER , sizeof( unsigned long *) );
PhastaIOActiveFiles[i]->my_read_table =
( unsigned long ** ) calloc( MAX_FIELDS_NUMBER , sizeof( unsigned long *) );
for (j=0; j<*nfields; j++)
{
PhastaIOActiveFiles[i]->my_offset_table[j] =
( unsigned long * ) calloc( PhastaIOActiveFiles[i]->nppp , sizeof( unsigned long) );
PhastaIOActiveFiles[i]->my_read_table[j] =
( unsigned long * ) calloc( PhastaIOActiveFiles[i]->nppp , sizeof( unsigned long) );
}
*filehandle = i;
PhastaIOActiveFiles[i]->master_header = (char *)calloc(MasterHeaderSize,sizeof( char ));
PhastaIOActiveFiles[i]->double_chunk = (double *)calloc(1,sizeof( double ));
PhastaIOActiveFiles[i]->int_chunk = (int *)calloc(1,sizeof( int ));
PhastaIOActiveFiles[i]->read_double_chunk = (double *)calloc(1,sizeof( double ));
PhastaIOActiveFiles[i]->read_int_chunk = (int *)calloc(1,sizeof( int ));
// Time monitoring
endTimer(&timer_end);
printPerf("initphmpiiosub", timer_start, timer_end, 0, 0, "");
phprintf_0("Info initphmpiiosub: quiting function");
return i;
}
namespace {
enum {
DIR_MODE = S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH
};
bool my_mkdir(std::string name) {
if(name.empty())
return true;
errno = 0;
int err = mkdir(name.c_str(), DIR_MODE);
if ((err == -1) && (errno == EEXIST)) {
errno = 0;
err = 0;
return false;
}
assert(!err);
return true;
}
enum {
DIR_FANOUT = 2048
};
std::string getSubDirPrefix() {
if (phio_peers() <= DIR_FANOUT)
return string("");
int self = phio_self();
int subSelf = self % DIR_FANOUT;
int subGroup = self / DIR_FANOUT;
std::stringstream ss;
ss << subGroup << '/';
return ss.str();
}
}
/** open file for both POSIX and MPI-IO syncIO format.
*
* If it's old POSIX format, simply call posix fopen().
*
* If it's MPI-IO foramt:
* in "read" mode, it builds the header table that points to the offset of
* fields for parts;
* in "write" mode, it opens the file with MPI-IO open routine.
*/
void openfile(const char filename[], const char mode[], int* fileDescriptor )
{
phprintf_0("Info: entering openfile");
double timer_start, timer_end;
startTimer(&timer_start);
if ( PhastaIONextActiveIndex == 0 )
{
FILE* file=NULL ;
*fileDescriptor = 0;
char* fname = StringStripper( filename );
char* imode = StringStripper( mode );
std::string posixname = getSubDirPrefix();
if (!phio_self())
my_mkdir(posixname);
phio_barrier();
posixname += string(fname);
if ( cscompare( "read", imode ) )
PHASTAIO_OPENTIME(file = fopen(posixname.c_str(), "rb" );)
else if( cscompare( "write", imode ) )
PHASTAIO_OPENTIME(file = fopen(posixname.c_str(), "wb" );)
else if( cscompare( "append", imode ) )
PHASTAIO_OPENTIME(file = fopen(posixname.c_str(), "ab" );)
if ( !file ){
fprintf(stderr,"Error openfile: unable to open file %s\n",fname);
} else {
fileArray.push_back( file );
byte_order.push_back( false );
header_type.push_back( sizeof(int) );
*fileDescriptor = fileArray.size();
}
free (fname);
free (imode);
}
else // else it would be parallel I/O, opposed to posix io
{
char* fname = StringStripper( filename );
char* imode = StringStripper( mode );
int rc;
int i = *fileDescriptor;
checkFileDescriptor("openfile",&i);
char* token;
if ( cscompare( "read", imode ) )
{
// if (PhastaIOActiveFiles[i]->myrank == 0)
// printf("\n **********\nRead open ... ... regular version\n");
PHASTAIO_OPENTIME(
rc = MPI_File_open( PhastaIOActiveFiles[i]->local_comm,
fname,
MPI_MODE_RDONLY,
MPI_INFO_NULL,
&(PhastaIOActiveFiles[i]->file_handle) );
)
if(rc)
{
*fileDescriptor = UNABLE_TO_OPEN_FILE;
int error_string_length;
char error_string[4096];
MPI_Error_string(rc, error_string, &error_string_length);
fprintf(stderr, "Error openfile: Unable to open file %s! MPI reports \"%s\"\n",fname,error_string);
endTimer(&timer_end);
printPerf("openfile", timer_start, timer_end, 0, 0, "");
return;
}
MPI_Status read_tag_status;
char read_out_tag[MAX_FIELDS_NAME_LENGTH];
int j;
int magic_number;
if ( PhastaIOActiveFiles[i]->local_myrank == 0 ) {
MPI_File_read_at( PhastaIOActiveFiles[i]->file_handle,
0,
PhastaIOActiveFiles[i]->master_header,
MasterHeaderSize,
MPI_CHAR,
&read_tag_status );
}