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GenericIO.cxx
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GenericIO.cxx
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/*
* Copyright (C) 2015, UChicago Argonne, LLC
* All Rights Reserved
*
* Generic IO (ANL-15-066)
* Hal Finkel, Argonne National Laboratory
*
* OPEN SOURCE LICENSE
*
* Under the terms of Contract No. DE-AC02-06CH11357 with UChicago Argonne,
* LLC, the U.S. Government retains certain rights in this software.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the distribution.
*
* 3. Neither the names of UChicago Argonne, LLC or the Department of Energy
* nor the names of its contributors may be used to endorse or promote
* products derived from this software without specific prior written
* permission.
*
* *****************************************************************************
*
* DISCLAIMER
* THE SOFTWARE IS SUPPLIED “AS IS” WITHOUT WARRANTY OF ANY KIND. NEITHER THE
* UNTED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT OF ENERGY, NOR
* UCHICAGO ARGONNE, LLC, NOR ANY OF THEIR EMPLOYEES, MAKES ANY WARRANTY,
* EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR RESPONSIBILITY FOR THE
* ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY INFORMATION, DATA, APPARATUS,
* PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE WOULD NOT INFRINGE
* PRIVATELY OWNED RIGHTS.
*
* *****************************************************************************
*/
#define _XOPEN_SOURCE 600
#include "CRC64.h"
#include "GenericIO.h"
extern "C" {
#include "blosc.h"
}
#include <sstream>
#include <fstream>
#include <stdexcept>
#include <iterator>
#include <algorithm>
#include <cassert>
#include <cstddef>
#include <cstring>
#ifndef GENERICIO_NO_MPI
#include <ctime>
#endif
#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <errno.h>
#ifdef __bgq__
#include <mpix.h>
#endif
#ifndef MPI_UINT64_T
#define MPI_UINT64_T (sizeof(long) == 8 ? MPI_LONG : MPI_LONG_LONG)
#endif
using namespace std;
namespace gio {
#ifndef GENERICIO_NO_MPI
GenericFileIO_MPI::~GenericFileIO_MPI() {
(void) MPI_File_close(&FH);
}
void GenericFileIO_MPI::open(const std::string &FN, bool ForReading) {
FileName = FN;
int commRank;
MPI_Comm_rank(MPI_COMM_WORLD, &commRank);
printf("OPEN %s %d \n", const_cast<char *>(FileName.c_str()), commRank);
int amode = ForReading ? MPI_MODE_RDONLY : (MPI_MODE_WRONLY | MPI_MODE_CREATE);
if (MPI_File_open(Comm, const_cast<char *>(FileName.c_str()), amode,
MPI_INFO_NULL, &FH) != MPI_SUCCESS)
throw runtime_error((!ForReading ? "Unable to create the file: " :
"Unable to open the file: ") +
FileName);
}
void GenericFileIO_MPI::setSize(size_t sz) {
if (MPI_File_set_size(FH, sz) != MPI_SUCCESS)
throw runtime_error("Unable to set size for file: " + FileName);
}
void GenericFileIO_MPI::read(void *buf, size_t count, off_t offset,
const std::string &D) {
while (count > 0) {
MPI_Status status;
if (MPI_File_read_at(FH, offset, buf, count, MPI_BYTE, &status) != MPI_SUCCESS)
throw runtime_error("Unable to read " + D + " from file: " + FileName);
int scount;
(void) MPI_Get_count(&status, MPI_BYTE, &scount);
count -= scount;
buf = ((char *) buf) + scount;
offset += scount;
}
}
void GenericFileIO_MPI::write(const void *buf, size_t count, off_t offset,
const std::string &D) {
int commRank;
MPI_Comm_rank(MPI_COMM_WORLD, &commRank);
//printf("RANK: %lu MPI_File_write_at %ld \n", commRank, count);
while (count > 0) {
MPI_Status status;
if (MPI_File_write_at(FH, offset, (void *) buf, count, MPI_BYTE, &status) != MPI_SUCCESS)
throw runtime_error("Unable to write " + D + " to file: " + FileName);
int scount = 0;
// On some systems, MPI_Get_count will not return zero even when count is zero.
if (count > 0)
(void) MPI_Get_count(&status, MPI_BYTE, &scount);
count -= scount;
buf = ((char *) buf) + scount;
offset += scount;
}
}
void GenericFileIO_MPICollective::read(void *buf, size_t count, off_t offset,
const std::string &D) {
int Continue = 0;
do {
MPI_Status status;
if (MPI_File_read_at_all(FH, offset, buf, count, MPI_BYTE, &status) != MPI_SUCCESS)
throw runtime_error("Unable to read " + D + " from file: " + FileName);
int scount = 0;
// On some systems, MPI_Get_count will not return zero even when count is zero.
if (count > 0)
(void) MPI_Get_count(&status, MPI_BYTE, &scount);
count -= scount;
buf = ((char *) buf) + scount;
offset += scount;
int NeedContinue = (count > 0);
MPI_Allreduce(&NeedContinue, &Continue, 1, MPI_INT, MPI_SUM, Comm);
} while (Continue);
}
void GenericFileIO_MPICollective::write(const void *buf, size_t count, off_t offset,
const std::string &D) {
int Continue = 0;
do {
MPI_Status status;
if (MPI_File_write_at_all(FH, offset, (void *) buf, count, MPI_BYTE, &status) != MPI_SUCCESS)
throw runtime_error("Unable to write " + D + " to file: " + FileName);
int scount;
(void) MPI_Get_count(&status, MPI_BYTE, &scount);
count -= scount;
buf = ((char *) buf) + scount;
offset += scount;
int NeedContinue = (count > 0);
MPI_Allreduce(&NeedContinue, &Continue, 1, MPI_INT, MPI_SUM, Comm);
} while (Continue);
}
#endif
GenericFileIO_POSIX::~GenericFileIO_POSIX() {
if (FH != -1) close(FH);
}
void GenericFileIO_POSIX::open(const std::string &FN, bool ForReading) {
FileName = FN;
int flags = ForReading ? O_RDONLY : (O_WRONLY | O_CREAT);
int mode = S_IRUSR | S_IWUSR | S_IRGRP;
errno = 0;
if ((FH = ::open(FileName.c_str(), flags, mode)) == -1)
throw runtime_error((!ForReading ? "Unable to create the file: " :
"Unable to open the file: ") +
FileName + ": " + strerror(errno));
}
void GenericFileIO_POSIX::setSize(size_t sz) {
if (ftruncate(FH, sz) == -1)
throw runtime_error("Unable to set size for file: " + FileName);
}
void GenericFileIO_POSIX::read(void *buf, size_t count, off_t offset,
const std::string &D) {
while (count > 0) {
ssize_t scount;
errno = 0;
if ((scount = pread(FH, buf, count, offset)) == -1) {
if (errno == EINTR)
continue;
throw runtime_error("Unable to read " + D + " from file: " + FileName +
": " + strerror(errno));
}
count -= scount;
buf = ((char *) buf) + scount;
offset += scount;
}
}
void GenericFileIO_POSIX::write(const void *buf, size_t count, off_t offset,
const std::string &D) {
while (count > 0) {
ssize_t scount;
errno = 0;
pid_t pid = getpid();
// printf("pid: %lu pwrite \n", pid);
if ((scount = pwrite(FH, buf, count, offset)) == -1) {
if (errno == EINTR)
continue;
throw runtime_error("Unable to write " + D + " to file: " + FileName +
": " + strerror(errno));
}
count -= scount;
buf = ((char *) buf) + scount;
offset += scount;
}
}
static bool isBigEndian() {
const uint32_t one = 1;
return !(*((char *)(&one)));
}
static void bswap(void *v, size_t s) {
char *p = (char *) v;
for (size_t i = 0; i < s/2; ++i)
std::swap(p[i], p[s - (i+1)]);
}
// Using #pragma pack here, instead of __attribute__((packed)) because xlc, at
// least as of v12.1, won't take __attribute__((packed)) on non-POD and/or
// templated types.
#pragma pack(1)
template <typename T, bool IsBigEndian>
struct endian_specific_value {
operator T() const {
T rvalue = value;
if (IsBigEndian != isBigEndian())
bswap(&rvalue, sizeof(T));
return rvalue;
};
endian_specific_value &operator = (T nvalue) {
if (IsBigEndian != isBigEndian())
bswap(&nvalue, sizeof(T));
value = nvalue;
return *this;
}
endian_specific_value &operator += (T nvalue) {
*this = *this + nvalue;
return *this;
}
endian_specific_value &operator -= (T nvalue) {
*this = *this - nvalue;
return *this;
}
private:
T value;
};
static const size_t CRCSize = 8;
static const size_t MagicSize = 8;
static const char *MagicBE = "HACC01B";
static const char *MagicLE = "HACC01L";
template <bool IsBigEndian>
struct GlobalHeader {
char Magic[MagicSize];
endian_specific_value<uint64_t, IsBigEndian> HeaderSize;
endian_specific_value<uint64_t, IsBigEndian> NElems; // The global total
endian_specific_value<uint64_t, IsBigEndian> Dims[3];
endian_specific_value<uint64_t, IsBigEndian> NVars;
endian_specific_value<uint64_t, IsBigEndian> VarsSize;
endian_specific_value<uint64_t, IsBigEndian> VarsStart;
endian_specific_value<uint64_t, IsBigEndian> NRanks;
endian_specific_value<uint64_t, IsBigEndian> RanksSize;
endian_specific_value<uint64_t, IsBigEndian> RanksStart;
endian_specific_value<uint64_t, IsBigEndian> GlobalHeaderSize;
endian_specific_value<double, IsBigEndian> PhysOrigin[3];
endian_specific_value<double, IsBigEndian> PhysScale[3];
endian_specific_value<uint64_t, IsBigEndian> BlocksSize;
endian_specific_value<uint64_t, IsBigEndian> BlocksStart;
};
enum {
FloatValue = (1 << 0),
SignedValue = (1 << 1),
ValueIsPhysCoordX = (1 << 2),
ValueIsPhysCoordY = (1 << 3),
ValueIsPhysCoordZ = (1 << 4),
ValueMaybePhysGhost = (1 << 5)
};
static const size_t NameSize = 256;
template <bool IsBigEndian>
struct VariableHeader {
char Name[NameSize];
endian_specific_value<uint64_t, IsBigEndian> Flags;
endian_specific_value<uint64_t, IsBigEndian> Size;
endian_specific_value<uint64_t, IsBigEndian> ElementSize;
};
template <bool IsBigEndian>
struct RankHeader {
endian_specific_value<uint64_t, IsBigEndian> Coords[3];
endian_specific_value<uint64_t, IsBigEndian> NElems;
endian_specific_value<uint64_t, IsBigEndian> Start;
endian_specific_value<uint64_t, IsBigEndian> GlobalRank;
};
static const size_t FilterNameSize = 8;
static const size_t MaxFilters = 4;
template <bool IsBigEndian>
struct BlockHeader {
char Filters[MaxFilters][FilterNameSize];
endian_specific_value<uint64_t, IsBigEndian> Start;
endian_specific_value<uint64_t, IsBigEndian> Size;
};
template <bool IsBigEndian>
struct CompressHeader {
endian_specific_value<uint64_t, IsBigEndian> OrigCRC;
};
const char *CompressName = "BLOSC";
#pragma pack()
unsigned GenericIO::DefaultFileIOType = FileIOPOSIX;
int GenericIO::DefaultPartition = 0;
bool GenericIO::DefaultShouldCompress = false;
#ifndef GENERICIO_NO_MPI
std::size_t GenericIO::CollectiveMPIIOThreshold = 0;
#endif
static bool blosc_initialized = false;
#ifndef GENERICIO_NO_MPI
void GenericIO::write() {
if (isBigEndian())
write<true>();
else
write<false>();
}
// Note: writing errors are not currently recoverable (one rank may fail
// while the others don't).
template <bool IsBigEndian>
void GenericIO::write() {
const char *Magic = IsBigEndian ? MagicBE : MagicLE;
uint64_t FileSize = 0;
int NRanks, Rank;
MPI_Comm_rank(Comm, &Rank);
MPI_Comm_size(Comm, &NRanks);
#ifdef __bgq__
MPI_Barrier(Comm);
#endif
MPI_Comm_split(Comm, Partition, Rank, &SplitComm);
int SplitNRanks, SplitRank;
MPI_Comm_rank(SplitComm, &SplitRank);
MPI_Comm_size(SplitComm, &SplitNRanks);
// printf("NUMBER %d %d\n",SplitRank, SplitNRanks);
string LocalFileName;
if (SplitNRanks != NRanks) {
if (Rank == 0) {
// In split mode, the specified file becomes the rank map, and the real
// data is partitioned.
vector<int> MapRank, MapPartition;
MapRank.resize(NRanks);
for (int i = 0; i < NRanks; ++i) MapRank[i] = i;
MapPartition.resize(NRanks);
MPI_Gather(&Partition, 1, MPI_INT, &MapPartition[0], 1, MPI_INT, 0, Comm);
GenericIO GIO(MPI_COMM_SELF, FileName, FileIOType);
GIO.setNumElems(NRanks);
GIO.addVariable("$rank", MapRank); /* this is for use by humans; the reading
code assumes that the partitions are in
rank order */
GIO.addVariable("$partition", MapPartition);
vector<int> CX, CY, CZ;
int TopoStatus;
MPI_Topo_test(Comm, &TopoStatus);
if (TopoStatus == MPI_CART) {
CX.resize(NRanks);
CY.resize(NRanks);
CZ.resize(NRanks);
for (int i = 0; i < NRanks; ++i) {
int C[3];
MPI_Cart_coords(Comm, i, 3, C);
CX[i] = C[0];
CY[i] = C[1];
CZ[i] = C[2];
}
GIO.addVariable("$x", CX);
GIO.addVariable("$y", CY);
GIO.addVariable("$z", CZ);
}
GIO.write();
} else {
MPI_Gather(&Partition, 1, MPI_INT, 0, 0, MPI_INT, 0, Comm);
}
//cout << FileName << endl;
stringstream ss;
ss << FileName << "#" << Partition;
LocalFileName = ss.str();
} else {
LocalFileName = FileName;
}
RankHeader<IsBigEndian> RHLocal;
int Dims[3], Periods[3], Coords[3];
int TopoStatus;
MPI_Topo_test(Comm, &TopoStatus);
if (TopoStatus == MPI_CART) {
MPI_Cart_get(Comm, 3, Dims, Periods, Coords);
} else {
Dims[0] = NRanks;
std::fill(Dims + 1, Dims + 3, 1);
std::fill(Periods, Periods + 3, 0);
Coords[0] = Rank;
std::fill(Coords + 1, Coords + 3, 0);
}
std::copy(Coords, Coords + 3, RHLocal.Coords);
RHLocal.NElems = NElems;
RHLocal.Start = 0;
RHLocal.GlobalRank = Rank;
bool ShouldCompress = DefaultShouldCompress;
const char *EnvStr = getenv("GENERICIO_COMPRESS");
if (EnvStr) {
int Mod = atoi(EnvStr);
ShouldCompress = (Mod > 0);
}
bool NeedsBlockHeaders = ShouldCompress;
EnvStr = getenv("GENERICIO_FORCE_BLOCKS");
if (!NeedsBlockHeaders && EnvStr) {
int Mod = atoi(EnvStr);
NeedsBlockHeaders = (Mod > 0);
}
vector<BlockHeader<IsBigEndian> > LocalBlockHeaders;
vector<void *> LocalData;
vector<bool> LocalHasExtraSpace;
vector<vector<unsigned char> > LocalCData;
if (NeedsBlockHeaders) {
LocalBlockHeaders.resize(Vars.size());
LocalData.resize(Vars.size());
LocalHasExtraSpace.resize(Vars.size());
if (ShouldCompress)
LocalCData.resize(Vars.size());
for (size_t i = 0; i < Vars.size(); ++i) {
// Filters null by default, leave null starting address (needs to be
// calculated by the header-writing rank).
memset(&LocalBlockHeaders[i], 0, sizeof(BlockHeader<IsBigEndian>));
if (ShouldCompress) {
LocalCData[i].resize(sizeof(CompressHeader<IsBigEndian>));
CompressHeader<IsBigEndian> *CH = (CompressHeader<IsBigEndian>*) &LocalCData[i][0];
CH->OrigCRC = crc64_omp(Vars[i].Data, Vars[i].Size*NElems);
#ifdef _OPENMP
#pragma omp master
{
#endif
if (!blosc_initialized) {
blosc_init();
blosc_initialized = true;
}
#ifdef _OPENMP
blosc_set_nthreads(omp_get_max_threads());
}
#endif
LocalCData[i].resize(LocalCData[i].size() + NElems*Vars[i].Size);
if (blosc_compress(9, 1, Vars[i].Size, NElems*Vars[i].Size, Vars[i].Data,
&LocalCData[i][0] + sizeof(CompressHeader<IsBigEndian>),
NElems*Vars[i].Size) <= 0)
goto nocomp;
strncpy(LocalBlockHeaders[i].Filters[0], CompressName, FilterNameSize);
size_t CNBytes, CCBytes, CBlockSize;
blosc_cbuffer_sizes(&LocalCData[i][0] + sizeof(CompressHeader<IsBigEndian>),
&CNBytes, &CCBytes, &CBlockSize);
LocalCData[i].resize(CCBytes + sizeof(CompressHeader<IsBigEndian>));
LocalBlockHeaders[i].Size = LocalCData[i].size();
LocalCData[i].resize(LocalCData[i].size() + CRCSize);
LocalData[i] = &LocalCData[i][0];
LocalHasExtraSpace[i] = true;
} else {
nocomp:
LocalBlockHeaders[i].Size = NElems*Vars[i].Size;
LocalData[i] = Vars[i].Data;
LocalHasExtraSpace[i] = Vars[i].HasExtraSpace;
}
}
}
double StartTime = MPI_Wtime();
if (SplitRank == 0) {
// printf("inside split rank %d %d\n",SplitRank, SplitNRanks);
uint64_t HeaderSize = sizeof(GlobalHeader<IsBigEndian>) + Vars.size()*sizeof(VariableHeader<IsBigEndian>) +
SplitNRanks*sizeof(RankHeader<IsBigEndian>) + CRCSize;
if (NeedsBlockHeaders)
HeaderSize += SplitNRanks*Vars.size()*sizeof(BlockHeader<IsBigEndian>);
vector<char> Header(HeaderSize, 0);
GlobalHeader<IsBigEndian> *GH = (GlobalHeader<IsBigEndian> *) &Header[0];
std::copy(Magic, Magic + MagicSize, GH->Magic);
GH->HeaderSize = HeaderSize - CRCSize;
GH->NElems = NElems; // This will be updated later
std::copy(Dims, Dims + 3, GH->Dims);
GH->NVars = Vars.size();
GH->VarsSize = sizeof(VariableHeader<IsBigEndian>);
GH->VarsStart = sizeof(GlobalHeader<IsBigEndian>);
GH->NRanks = SplitNRanks;
GH->RanksSize = sizeof(RankHeader<IsBigEndian>);
GH->RanksStart = GH->VarsStart + Vars.size()*sizeof(VariableHeader<IsBigEndian>);
GH->GlobalHeaderSize = sizeof(GlobalHeader<IsBigEndian>);
std::copy(PhysOrigin, PhysOrigin + 3, GH->PhysOrigin);
std::copy(PhysScale, PhysScale + 3, GH->PhysScale);
if (!NeedsBlockHeaders) {
GH->BlocksSize = GH->BlocksStart = 0;
} else {
GH->BlocksSize = sizeof(BlockHeader<IsBigEndian>);
GH->BlocksStart = GH->RanksStart + SplitNRanks*sizeof(RankHeader<IsBigEndian>);
}
uint64_t RecordSize = 0;
VariableHeader<IsBigEndian> *VH = (VariableHeader<IsBigEndian> *) &Header[GH->VarsStart];
for (size_t i = 0; i < Vars.size(); ++i, ++VH) {
string VName(Vars[i].Name);
VName.resize(NameSize);
std::copy(VName.begin(), VName.end(), VH->Name);
uint64_t VFlags = 0;
if (Vars[i].IsFloat) VFlags |= FloatValue;
if (Vars[i].IsSigned) VFlags |= SignedValue;
if (Vars[i].IsPhysCoordX) VFlags |= ValueIsPhysCoordX;
if (Vars[i].IsPhysCoordY) VFlags |= ValueIsPhysCoordY;
if (Vars[i].IsPhysCoordZ) VFlags |= ValueIsPhysCoordZ;
if (Vars[i].MaybePhysGhost) VFlags |= ValueMaybePhysGhost;
VH->Flags = VFlags;
RecordSize += VH->Size = Vars[i].Size;
VH->ElementSize = Vars[i].ElementSize;
}
MPI_Gather(&RHLocal, sizeof(RHLocal), MPI_BYTE,
&Header[GH->RanksStart], sizeof(RHLocal),
MPI_BYTE, 0, SplitComm);
if (NeedsBlockHeaders) {
MPI_Gather(&LocalBlockHeaders[0],
Vars.size()*sizeof(BlockHeader<IsBigEndian>), MPI_BYTE,
&Header[GH->BlocksStart],
Vars.size()*sizeof(BlockHeader<IsBigEndian>), MPI_BYTE,
0, SplitComm);
BlockHeader<IsBigEndian> *BH = (BlockHeader<IsBigEndian> *) &Header[GH->BlocksStart];
for (int i = 0; i < SplitNRanks; ++i)
for (size_t j = 0; j < Vars.size(); ++j, ++BH) {
if (i == 0 && j == 0)
BH->Start = HeaderSize;
else
BH->Start = BH[-1].Start + BH[-1].Size + CRCSize;
}
RankHeader<IsBigEndian> *RH = (RankHeader<IsBigEndian> *) &Header[GH->RanksStart];
RH->Start = HeaderSize; ++RH;
for (int i = 1; i < SplitNRanks; ++i, ++RH) {
RH->Start =
((BlockHeader<IsBigEndian> *) &Header[GH->BlocksStart])[i*Vars.size()].Start;
GH->NElems += RH->NElems;
}
// Compute the total file size.
uint64_t LastData = BH[-1].Size + CRCSize;
FileSize = BH[-1].Start + LastData;
} else {
RankHeader<IsBigEndian> *RH = (RankHeader<IsBigEndian> *) &Header[GH->RanksStart];
RH->Start = HeaderSize; ++RH;
for (int i = 1; i < SplitNRanks; ++i, ++RH) {
uint64_t PrevNElems = RH[-1].NElems;
uint64_t PrevData = PrevNElems*RecordSize + CRCSize*Vars.size();
RH->Start = RH[-1].Start + PrevData;
GH->NElems += RH->NElems;
}
// Compute the total file size.
uint64_t LastNElems = RH[-1].NElems;
uint64_t LastData = LastNElems*RecordSize + CRCSize*Vars.size();
FileSize = RH[-1].Start + LastData;
}
// Now that the starting offset has been computed, send it back to each rank.
MPI_Scatter(&Header[GH->RanksStart], sizeof(RHLocal),
MPI_BYTE, &RHLocal, sizeof(RHLocal),
MPI_BYTE, 0, SplitComm);
if (NeedsBlockHeaders)
MPI_Scatter(&Header[GH->BlocksStart],
sizeof(BlockHeader<IsBigEndian>)*Vars.size(), MPI_BYTE,
&LocalBlockHeaders[0],
sizeof(BlockHeader<IsBigEndian>)*Vars.size(), MPI_BYTE,
0, SplitComm);
uint64_t HeaderCRC = crc64_omp(&Header[0], HeaderSize - CRCSize);
crc64_invert(HeaderCRC, &Header[HeaderSize - CRCSize]);
if (FileIOType == FileIOMPI)
FH.get() = new GenericFileIO_MPI(MPI_COMM_SELF);
else if (FileIOType == FileIOMPICollective)
FH.get() = new GenericFileIO_MPICollective(MPI_COMM_SELF);
else
FH.get() = new GenericFileIO_POSIX();
FH.get()->open(LocalFileName);
FH.get()->setSize(FileSize);
FH.get()->write(&Header[0], HeaderSize, 0, "header");
close();
} else {
MPI_Gather(&RHLocal, sizeof(RHLocal), MPI_BYTE, 0, 0, MPI_BYTE, 0, SplitComm);
if (NeedsBlockHeaders)
MPI_Gather(&LocalBlockHeaders[0], Vars.size()*sizeof(BlockHeader<IsBigEndian>),
MPI_BYTE, 0, 0, MPI_BYTE, 0, SplitComm);
MPI_Scatter(0, 0, MPI_BYTE, &RHLocal, sizeof(RHLocal), MPI_BYTE, 0, SplitComm);
if (NeedsBlockHeaders)
MPI_Scatter(0, 0, MPI_BYTE, &LocalBlockHeaders[0], sizeof(BlockHeader<IsBigEndian>)*Vars.size(),
MPI_BYTE, 0, SplitComm);
}
MPI_Barrier(SplitComm);
if (FileIOType == FileIOMPI)
FH.get() = new GenericFileIO_MPI(SplitComm);
else if (FileIOType == FileIOMPICollective)
FH.get() = new GenericFileIO_MPICollective(SplitComm);
else
FH.get() = new GenericFileIO_POSIX();
FH.get()->open(LocalFileName);
uint64_t Offset = RHLocal.Start;
for (size_t i = 0; i < Vars.size(); ++i) {
uint64_t WriteSize = NeedsBlockHeaders ?
LocalBlockHeaders[i].Size : NElems*Vars[i].Size;
void *Data = NeedsBlockHeaders ? LocalData[i] : Vars[i].Data;
uint64_t CRC = crc64_omp(Data, WriteSize);
bool HasExtraSpace = NeedsBlockHeaders ?
LocalHasExtraSpace[i] : Vars[i].HasExtraSpace;
char *CRCLoc = HasExtraSpace ? ((char *) Data) + WriteSize : (char *) &CRC;
if (NeedsBlockHeaders)
Offset = LocalBlockHeaders[i].Start;
// When using extra space for the CRC write, preserve the original contents.
char CRCSave[CRCSize];
if (HasExtraSpace)
std::copy(CRCLoc, CRCLoc + CRCSize, CRCSave);
crc64_invert(CRC, CRCLoc);
if (HasExtraSpace) {
FH.get()->write(Data, WriteSize + CRCSize, Offset, Vars[i].Name + " with CRC");
} else {
FH.get()->write(Data, WriteSize, Offset, Vars[i].Name);
FH.get()->write(CRCLoc, CRCSize, Offset + WriteSize, Vars[i].Name + " CRC");
}
if (HasExtraSpace)
std::copy(CRCSave, CRCSave + CRCSize, CRCLoc);
Offset += WriteSize + CRCSize;
}
close();
MPI_Barrier(Comm);
double EndTime = MPI_Wtime();
double TotalTime = EndTime - StartTime;
double MaxTotalTime;
MPI_Reduce(&TotalTime, &MaxTotalTime, 1, MPI_DOUBLE, MPI_MAX, 0, Comm);
if (SplitNRanks != NRanks) {
uint64_t ContribFileSize = (SplitRank == 0) ? FileSize : 0;
MPI_Reduce(&ContribFileSize, &FileSize, 1, MPI_UINT64_T, MPI_SUM, 0, Comm);
}
if (Rank == 0) {
double Rate = ((double) FileSize) / MaxTotalTime / (1024.*1024.);
cout << "Wrote " << Vars.size() << " variables to " << FileName <<
" (" << FileSize << " bytes) in " << MaxTotalTime << "s: " <<
Rate << " MB/s" << endl;
}
MPI_Comm_free(&SplitComm);
SplitComm = MPI_COMM_NULL;
}
#endif // GENERICIO_NO_MPI
template <bool IsBigEndian>
void GenericIO::readHeaderLeader(void *GHPtr, MismatchBehavior MB, int NRanks,
int Rank, int SplitNRanks,
string &LocalFileName, uint64_t &HeaderSize,
vector<char> &Header) {
GlobalHeader<IsBigEndian> &GH = *(GlobalHeader<IsBigEndian> *) GHPtr;
if (MB == MismatchDisallowed) {
if (SplitNRanks != (int) GH.NRanks) {
stringstream ss;
ss << "Won't read " << LocalFileName << ": communicator-size mismatch: " <<
"current: " << SplitNRanks << ", file: " << GH.NRanks;
throw runtime_error(ss.str());
}
#ifndef GENERICIO_NO_MPI
int TopoStatus;
MPI_Topo_test(Comm, &TopoStatus);
if (TopoStatus == MPI_CART) {
int Dims[3], Periods[3], Coords[3];
MPI_Cart_get(Comm, 3, Dims, Periods, Coords);
bool DimsMatch = true;
for (int i = 0; i < 3; ++i) {
if ((uint64_t) Dims[i] != GH.Dims[i]) {
DimsMatch = false;
break;
}
}
if (!DimsMatch) {
stringstream ss;
ss << "Won't read " << LocalFileName <<
": communicator-decomposition mismatch: " <<
"current: " << Dims[0] << "x" << Dims[1] << "x" << Dims[2] <<
", file: " << GH.Dims[0] << "x" << GH.Dims[1] << "x" <<
GH.Dims[2];
throw runtime_error(ss.str());
}
}
#endif
} else if (MB == MismatchRedistribute && !Redistributing) {
Redistributing = true;
int NFileRanks = RankMap.empty() ? (int) GH.NRanks : (int) RankMap.size();
int NFileRanksPerRank = NFileRanks/NRanks;
int NRemFileRank = NFileRanks % NRanks;
if (!NFileRanksPerRank) {
// We have only the remainder, so the last NRemFileRank ranks get one
// file rank, and the others don't.
if (NRemFileRank && NRanks - Rank <= NRemFileRank)
SourceRanks.push_back(NRanks - (Rank + 1));
} else {
// Since NRemFileRank < NRanks, and we don't want to put any extra memory
// load on rank 0 (because rank 0's memory load is normally higher than
// the other ranks anyway), the last NRemFileRank will each take
// (NFileRanksPerRank+1) file ranks.
int FirstFileRank = 0, LastFileRank = NFileRanksPerRank - 1;
for (int i = 1; i <= Rank; ++i) {
FirstFileRank = LastFileRank + 1;
LastFileRank = FirstFileRank + NFileRanksPerRank - 1;
if (NRemFileRank && NRanks - i <= NRemFileRank)
++LastFileRank;
}
for (int i = FirstFileRank; i <= LastFileRank; ++i)
SourceRanks.push_back(i);
}
}
HeaderSize = GH.HeaderSize;
Header.resize(HeaderSize + CRCSize, 0xFE /* poison */);
FH.get()->read(&Header[0], HeaderSize + CRCSize, 0, "header");
uint64_t CRC = crc64_omp(&Header[0], HeaderSize + CRCSize);
if (CRC != (uint64_t) -1) {
throw runtime_error("Header CRC check failed: " + LocalFileName);
}
}
// Note: Errors from this function should be recoverable. This means that if
// one rank throws an exception, then all ranks should.
void GenericIO::openAndReadHeader(MismatchBehavior MB, int EffRank, bool CheckPartMap) {
int NRanks, Rank;
#ifndef GENERICIO_NO_MPI
MPI_Comm_rank(Comm, &Rank);
MPI_Comm_size(Comm, &NRanks);
#else
Rank = 0;
NRanks = 1;
#endif
if (EffRank == -1)
EffRank = MB == MismatchRedistribute ? 0 : Rank;
if (RankMap.empty() && CheckPartMap) {
// First, check to see if the file is a rank map.
unsigned long RanksInMap = 0;
if (Rank == 0) {
try {
#ifndef GENERICIO_NO_MPI
GenericIO GIO(MPI_COMM_SELF, FileName, FileIOType);
#else
GenericIO GIO(FileName, FileIOType);
#endif
GIO.openAndReadHeader(MismatchDisallowed, 0, false);
RanksInMap = GIO.readNumElems();
RankMap.resize(RanksInMap + GIO.requestedExtraSpace()/sizeof(int));
GIO.addVariable("$partition", RankMap, true);
GIO.readData(0, false);
RankMap.resize(RanksInMap);
} catch (...) {
RankMap.clear();
RanksInMap = 0;
}
}
#ifndef GENERICIO_NO_MPI
MPI_Bcast(&RanksInMap, 1, MPI_UNSIGNED_LONG, 0, Comm);
if (RanksInMap > 0) {
RankMap.resize(RanksInMap);
MPI_Bcast(&RankMap[0], RanksInMap, MPI_INT, 0, Comm);
}
#endif
}
#ifndef GENERICIO_NO_MPI
if (SplitComm != MPI_COMM_NULL)
MPI_Comm_free(&SplitComm);
#endif
string LocalFileName;
if (RankMap.empty()) {
LocalFileName = FileName;
#ifndef GENERICIO_NO_MPI
MPI_Comm_dup(MB == MismatchRedistribute ? MPI_COMM_SELF : Comm, &SplitComm);
#endif
} else {
stringstream ss;
ss << FileName << "#" << RankMap[EffRank];
LocalFileName = ss.str();
#ifndef GENERICIO_NO_MPI
if (MB == MismatchRedistribute) {
MPI_Comm_dup(MPI_COMM_SELF, &SplitComm);
} else {
#ifdef __bgq__
MPI_Barrier(Comm);
#endif
MPI_Comm_split(Comm, RankMap[EffRank], Rank, &SplitComm);
}
#endif
}
if (LocalFileName == OpenFileName)
return;
FH.close();
int SplitNRanks, SplitRank;
#ifndef GENERICIO_NO_MPI
MPI_Comm_rank(SplitComm, &SplitRank);
MPI_Comm_size(SplitComm, &SplitNRanks);
#else
SplitRank = 0;
SplitNRanks = 1;
#endif
uint64_t HeaderSize;
vector<char> Header;
if (SplitRank == 0) {
#ifndef GENERICIO_NO_MPI
if (FileIOType == FileIOMPI)
FH.get() = new GenericFileIO_MPI(MPI_COMM_SELF);
else if (FileIOType == FileIOMPICollective)
FH.get() = new GenericFileIO_MPICollective(MPI_COMM_SELF);
else
#endif
FH.get() = new GenericFileIO_POSIX();
#ifndef GENERICIO_NO_MPI
char True = 1, False = 0;
#endif
try {
FH.get()->open(LocalFileName, true);
GlobalHeader<false> GH; // endianness does not matter yet...
FH.get()->read(&GH, sizeof(GlobalHeader<false>), 0, "global header");
if (string(GH.Magic, GH.Magic + MagicSize - 1) == MagicLE) {
readHeaderLeader<false>(&GH, MB, NRanks, Rank, SplitNRanks, LocalFileName,
HeaderSize, Header);
} else if (string(GH.Magic, GH.Magic + MagicSize - 1) == MagicBE) {
readHeaderLeader<true>(&GH, MB, NRanks, Rank, SplitNRanks, LocalFileName,
HeaderSize, Header);
} else {
string Error = "invalid file-type identifier";
throw runtime_error("Won't read " + LocalFileName + ": " + Error);
}
#ifndef GENERICIO_NO_MPI
close();
MPI_Bcast(&True, 1, MPI_BYTE, 0, SplitComm);
#endif
} catch (...) {
#ifndef GENERICIO_NO_MPI
MPI_Bcast(&False, 1, MPI_BYTE, 0, SplitComm);
#endif
close();
throw;
}
} else {
#ifndef GENERICIO_NO_MPI
char Okay;
MPI_Bcast(&Okay, 1, MPI_BYTE, 0, SplitComm);
if (!Okay)
throw runtime_error("Failure broadcast from rank 0");
#endif
}
#ifndef GENERICIO_NO_MPI
MPI_Bcast(&HeaderSize, 1, MPI_UINT64_T, 0, SplitComm);
#endif
Header.resize(HeaderSize, 0xFD /* poison */);
#ifndef GENERICIO_NO_MPI
MPI_Bcast(&Header[0], HeaderSize, MPI_BYTE, 0, SplitComm);
#endif
FH.getHeaderCache().clear();
GlobalHeader<false> *GH = (GlobalHeader<false> *) &Header[0];
FH.setIsBigEndian(string(GH->Magic, GH->Magic + MagicSize - 1) == MagicBE);