[da65757] | 1 | /* |
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| 2 | * Copyright (C) 2015, UChicago Argonne, LLC |
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| 3 | * All Rights Reserved |
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| 4 | * |
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| 5 | * Generic IO (ANL-15-066) |
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| 6 | * Hal Finkel, Argonne National Laboratory |
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| 7 | * |
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| 8 | * OPEN SOURCE LICENSE |
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| 9 | * |
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| 10 | * Under the terms of Contract No. DE-AC02-06CH11357 with UChicago Argonne, |
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| 11 | * LLC, the U.S. Government retains certain rights in this software. |
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| 12 | * |
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| 13 | * Redistribution and use in source and binary forms, with or without |
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| 14 | * modification, are permitted provided that the following conditions are met: |
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| 15 | * |
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| 16 | * 1. Redistributions of source code must retain the above copyright notice, |
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| 17 | * this list of conditions and the following disclaimer. |
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| 18 | * |
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| 19 | * 2. Redistributions in binary form must reproduce the above copyright |
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| 20 | * notice, this list of conditions and the following disclaimer in the |
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| 21 | * documentation and/or other materials provided with the distribution. |
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| 22 | * |
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| 23 | * 3. Neither the names of UChicago Argonne, LLC or the Department of Energy |
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| 24 | * nor the names of its contributors may be used to endorse or promote |
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| 25 | * products derived from this software without specific prior written |
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| 26 | * permission. |
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| 27 | * |
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| 28 | * ***************************************************************************** |
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| 29 | * |
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| 30 | * DISCLAIMER |
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| 31 | * THE SOFTWARE IS SUPPLIED “AS IS” WITHOUT WARRANTY OF ANY KIND. NEITHER THE |
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| 32 | * UNTED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT OF ENERGY, NOR |
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| 33 | * UCHICAGO ARGONNE, LLC, NOR ANY OF THEIR EMPLOYEES, MAKES ANY WARRANTY, |
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| 34 | * EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR RESPONSIBILITY FOR THE |
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| 35 | * ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY INFORMATION, DATA, APPARATUS, |
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| 36 | * PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE WOULD NOT INFRINGE |
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| 37 | * PRIVATELY OWNED RIGHTS. |
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| 38 | * |
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| 39 | * ***************************************************************************** |
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| 40 | */ |
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| 41 | |
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[00587dc] | 42 | #define _XOPEN_SOURCE 600 |
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| 43 | #include "CRC64.h" |
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| 44 | #include "GenericIO.h" |
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| 45 | |
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| 46 | extern "C" { |
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| 47 | #include "blosc.h" |
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| 48 | } |
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[6461f57] | 49 | #include "sz.h" |
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[00587dc] | 50 | |
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| 51 | #include <sstream> |
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| 52 | #include <fstream> |
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| 53 | #include <stdexcept> |
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[14e73bb] | 54 | #include <iterator> |
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[00587dc] | 55 | #include <algorithm> |
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| 56 | #include <cassert> |
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| 57 | #include <cstddef> |
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| 58 | #include <cstring> |
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| 59 | |
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| 60 | #ifndef GENERICIO_NO_MPI |
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| 61 | #include <ctime> |
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| 62 | #endif |
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| 63 | |
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| 64 | #include <sys/types.h> |
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| 65 | #include <sys/stat.h> |
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| 66 | #include <fcntl.h> |
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| 67 | #include <errno.h> |
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| 68 | |
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| 69 | #ifdef __bgq__ |
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[14e73bb] | 70 | #include <mpix.h> |
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[00587dc] | 71 | #endif |
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| 72 | |
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| 73 | #ifndef MPI_UINT64_T |
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| 74 | #define MPI_UINT64_T (sizeof(long) == 8 ? MPI_LONG : MPI_LONG_LONG) |
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| 75 | #endif |
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| 76 | |
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| 77 | using namespace std; |
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| 78 | |
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| 79 | namespace gio { |
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| 80 | |
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| 81 | |
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| 82 | #ifndef GENERICIO_NO_MPI |
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| 83 | GenericFileIO_MPI::~GenericFileIO_MPI() { |
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| 84 | (void) MPI_File_close(&FH); |
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| 85 | } |
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| 86 | |
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| 87 | void GenericFileIO_MPI::open(const std::string &FN, bool ForReading) { |
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| 88 | FileName = FN; |
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| 89 | |
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| 90 | int amode = ForReading ? MPI_MODE_RDONLY : (MPI_MODE_WRONLY | MPI_MODE_CREATE); |
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| 91 | if (MPI_File_open(Comm, const_cast<char *>(FileName.c_str()), amode, |
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| 92 | MPI_INFO_NULL, &FH) != MPI_SUCCESS) |
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| 93 | throw runtime_error((!ForReading ? "Unable to create the file: " : |
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| 94 | "Unable to open the file: ") + |
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| 95 | FileName); |
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| 96 | } |
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| 97 | |
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| 98 | void GenericFileIO_MPI::setSize(size_t sz) { |
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| 99 | if (MPI_File_set_size(FH, sz) != MPI_SUCCESS) |
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| 100 | throw runtime_error("Unable to set size for file: " + FileName); |
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| 101 | } |
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| 102 | |
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| 103 | void GenericFileIO_MPI::read(void *buf, size_t count, off_t offset, |
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| 104 | const std::string &D) { |
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| 105 | while (count > 0) { |
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| 106 | MPI_Status status; |
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| 107 | if (MPI_File_read_at(FH, offset, buf, count, MPI_BYTE, &status) != MPI_SUCCESS) |
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| 108 | throw runtime_error("Unable to read " + D + " from file: " + FileName); |
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| 109 | |
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| 110 | int scount; |
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| 111 | (void) MPI_Get_count(&status, MPI_BYTE, &scount); |
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| 112 | |
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| 113 | count -= scount; |
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| 114 | buf = ((char *) buf) + scount; |
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| 115 | offset += scount; |
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| 116 | } |
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| 117 | } |
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| 118 | |
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| 119 | void GenericFileIO_MPI::write(const void *buf, size_t count, off_t offset, |
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| 120 | const std::string &D) { |
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| 121 | while (count > 0) { |
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| 122 | MPI_Status status; |
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| 123 | if (MPI_File_write_at(FH, offset, (void *) buf, count, MPI_BYTE, &status) != MPI_SUCCESS) |
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| 124 | throw runtime_error("Unable to write " + D + " to file: " + FileName); |
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| 125 | |
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[56b997e] | 126 | int scount = 0; |
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| 127 | // On some systems, MPI_Get_count will not return zero even when count is zero. |
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| 128 | if (count > 0) |
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| 129 | (void) MPI_Get_count(&status, MPI_BYTE, &scount); |
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[00587dc] | 130 | |
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| 131 | count -= scount; |
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| 132 | buf = ((char *) buf) + scount; |
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| 133 | offset += scount; |
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| 134 | } |
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| 135 | } |
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| 136 | |
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| 137 | void GenericFileIO_MPICollective::read(void *buf, size_t count, off_t offset, |
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| 138 | const std::string &D) { |
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| 139 | int Continue = 0; |
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| 140 | |
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| 141 | do { |
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| 142 | MPI_Status status; |
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| 143 | if (MPI_File_read_at_all(FH, offset, buf, count, MPI_BYTE, &status) != MPI_SUCCESS) |
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| 144 | throw runtime_error("Unable to read " + D + " from file: " + FileName); |
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| 145 | |
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[56b997e] | 146 | int scount = 0; |
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| 147 | // On some systems, MPI_Get_count will not return zero even when count is zero. |
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| 148 | if (count > 0) |
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| 149 | (void) MPI_Get_count(&status, MPI_BYTE, &scount); |
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[00587dc] | 150 | |
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| 151 | count -= scount; |
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| 152 | buf = ((char *) buf) + scount; |
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| 153 | offset += scount; |
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| 154 | |
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| 155 | int NeedContinue = (count > 0); |
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| 156 | MPI_Allreduce(&NeedContinue, &Continue, 1, MPI_INT, MPI_SUM, Comm); |
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| 157 | } while (Continue); |
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| 158 | } |
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| 159 | |
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| 160 | void GenericFileIO_MPICollective::write(const void *buf, size_t count, off_t offset, |
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| 161 | const std::string &D) { |
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| 162 | int Continue = 0; |
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| 163 | |
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| 164 | do { |
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| 165 | MPI_Status status; |
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| 166 | if (MPI_File_write_at_all(FH, offset, (void *) buf, count, MPI_BYTE, &status) != MPI_SUCCESS) |
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| 167 | throw runtime_error("Unable to write " + D + " to file: " + FileName); |
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| 168 | |
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| 169 | int scount; |
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| 170 | (void) MPI_Get_count(&status, MPI_BYTE, &scount); |
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| 171 | |
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| 172 | count -= scount; |
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| 173 | buf = ((char *) buf) + scount; |
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| 174 | offset += scount; |
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| 175 | |
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| 176 | int NeedContinue = (count > 0); |
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| 177 | MPI_Allreduce(&NeedContinue, &Continue, 1, MPI_INT, MPI_SUM, Comm); |
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| 178 | } while (Continue); |
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| 179 | } |
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| 180 | #endif |
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| 181 | |
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| 182 | GenericFileIO_POSIX::~GenericFileIO_POSIX() { |
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| 183 | if (FH != -1) close(FH); |
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| 184 | } |
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| 185 | |
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| 186 | void GenericFileIO_POSIX::open(const std::string &FN, bool ForReading) { |
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| 187 | FileName = FN; |
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| 188 | |
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| 189 | int flags = ForReading ? O_RDONLY : (O_WRONLY | O_CREAT); |
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| 190 | int mode = S_IRUSR | S_IWUSR | S_IRGRP; |
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| 191 | errno = 0; |
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| 192 | if ((FH = ::open(FileName.c_str(), flags, mode)) == -1) |
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| 193 | throw runtime_error((!ForReading ? "Unable to create the file: " : |
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| 194 | "Unable to open the file: ") + |
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| 195 | FileName + ": " + strerror(errno)); |
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| 196 | } |
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| 197 | |
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| 198 | void GenericFileIO_POSIX::setSize(size_t sz) { |
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| 199 | if (ftruncate(FH, sz) == -1) |
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| 200 | throw runtime_error("Unable to set size for file: " + FileName); |
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| 201 | } |
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| 202 | |
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| 203 | void GenericFileIO_POSIX::read(void *buf, size_t count, off_t offset, |
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| 204 | const std::string &D) { |
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| 205 | while (count > 0) { |
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| 206 | ssize_t scount; |
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| 207 | errno = 0; |
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| 208 | if ((scount = pread(FH, buf, count, offset)) == -1) { |
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| 209 | if (errno == EINTR) |
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| 210 | continue; |
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| 211 | |
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[14e73bb] | 212 | throw runtime_error("Unable to read " + D + " from file: " + FileName + |
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| 213 | ": " + strerror(errno)); |
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[00587dc] | 214 | } |
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| 215 | |
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| 216 | count -= scount; |
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| 217 | buf = ((char *) buf) + scount; |
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| 218 | offset += scount; |
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| 219 | } |
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| 220 | } |
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| 221 | |
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| 222 | void GenericFileIO_POSIX::write(const void *buf, size_t count, off_t offset, |
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| 223 | const std::string &D) { |
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| 224 | while (count > 0) { |
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| 225 | ssize_t scount; |
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| 226 | errno = 0; |
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| 227 | if ((scount = pwrite(FH, buf, count, offset)) == -1) { |
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| 228 | if (errno == EINTR) |
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| 229 | continue; |
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| 230 | |
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[14e73bb] | 231 | throw runtime_error("Unable to write " + D + " to file: " + FileName + |
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| 232 | ": " + strerror(errno)); |
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[00587dc] | 233 | } |
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| 234 | |
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| 235 | count -= scount; |
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| 236 | buf = ((char *) buf) + scount; |
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| 237 | offset += scount; |
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| 238 | } |
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| 239 | } |
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| 240 | |
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| 241 | static bool isBigEndian() { |
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| 242 | const uint32_t one = 1; |
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| 243 | return !(*((char *)(&one))); |
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| 244 | } |
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| 245 | |
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[a4fee13] | 246 | static void bswap(void *v, size_t s) { |
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| 247 | char *p = (char *) v; |
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| 248 | for (size_t i = 0; i < s/2; ++i) |
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| 249 | std::swap(p[i], p[s - (i+1)]); |
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| 250 | } |
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| 251 | |
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| 252 | // Using #pragma pack here, instead of __attribute__((packed)) because xlc, at |
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| 253 | // least as of v12.1, won't take __attribute__((packed)) on non-POD and/or |
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| 254 | // templated types. |
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| 255 | #pragma pack(1) |
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| 256 | |
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| 257 | template <typename T, bool IsBigEndian> |
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| 258 | struct endian_specific_value { |
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| 259 | operator T() const { |
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| 260 | T rvalue = value; |
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| 261 | if (IsBigEndian != isBigEndian()) |
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| 262 | bswap(&rvalue, sizeof(T)); |
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| 263 | |
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| 264 | return rvalue; |
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| 265 | }; |
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| 266 | |
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| 267 | endian_specific_value &operator = (T nvalue) { |
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| 268 | if (IsBigEndian != isBigEndian()) |
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| 269 | bswap(&nvalue, sizeof(T)); |
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| 270 | |
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| 271 | value = nvalue; |
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| 272 | return *this; |
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| 273 | } |
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| 274 | |
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| 275 | endian_specific_value &operator += (T nvalue) { |
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| 276 | *this = *this + nvalue; |
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| 277 | return *this; |
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| 278 | } |
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| 279 | |
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| 280 | endian_specific_value &operator -= (T nvalue) { |
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| 281 | *this = *this - nvalue; |
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| 282 | return *this; |
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| 283 | } |
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| 284 | |
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| 285 | private: |
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| 286 | T value; |
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| 287 | }; |
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| 288 | |
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[00587dc] | 289 | static const size_t CRCSize = 8; |
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| 290 | |
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| 291 | static const size_t MagicSize = 8; |
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| 292 | static const char *MagicBE = "HACC01B"; |
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| 293 | static const char *MagicLE = "HACC01L"; |
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| 294 | |
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[a4fee13] | 295 | template <bool IsBigEndian> |
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[00587dc] | 296 | struct GlobalHeader { |
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| 297 | char Magic[MagicSize]; |
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[a4fee13] | 298 | endian_specific_value<uint64_t, IsBigEndian> HeaderSize; |
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| 299 | endian_specific_value<uint64_t, IsBigEndian> NElems; // The global total |
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| 300 | endian_specific_value<uint64_t, IsBigEndian> Dims[3]; |
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| 301 | endian_specific_value<uint64_t, IsBigEndian> NVars; |
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| 302 | endian_specific_value<uint64_t, IsBigEndian> VarsSize; |
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| 303 | endian_specific_value<uint64_t, IsBigEndian> VarsStart; |
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| 304 | endian_specific_value<uint64_t, IsBigEndian> NRanks; |
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| 305 | endian_specific_value<uint64_t, IsBigEndian> RanksSize; |
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| 306 | endian_specific_value<uint64_t, IsBigEndian> RanksStart; |
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| 307 | endian_specific_value<uint64_t, IsBigEndian> GlobalHeaderSize; |
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| 308 | endian_specific_value<double, IsBigEndian> PhysOrigin[3]; |
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| 309 | endian_specific_value<double, IsBigEndian> PhysScale[3]; |
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| 310 | endian_specific_value<uint64_t, IsBigEndian> BlocksSize; |
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| 311 | endian_specific_value<uint64_t, IsBigEndian> BlocksStart; |
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| 312 | }; |
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[00587dc] | 313 | |
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| 314 | enum { |
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| 315 | FloatValue = (1 << 0), |
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| 316 | SignedValue = (1 << 1), |
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| 317 | ValueIsPhysCoordX = (1 << 2), |
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| 318 | ValueIsPhysCoordY = (1 << 3), |
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| 319 | ValueIsPhysCoordZ = (1 << 4), |
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| 320 | ValueMaybePhysGhost = (1 << 5) |
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| 321 | }; |
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| 322 | |
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| 323 | static const size_t NameSize = 256; |
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[a4fee13] | 324 | template <bool IsBigEndian> |
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[00587dc] | 325 | struct VariableHeader { |
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| 326 | char Name[NameSize]; |
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[a4fee13] | 327 | endian_specific_value<uint64_t, IsBigEndian> Flags; |
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| 328 | endian_specific_value<uint64_t, IsBigEndian> Size; |
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[5d57155] | 329 | endian_specific_value<uint64_t, IsBigEndian> ElementSize; |
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[a4fee13] | 330 | }; |
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[00587dc] | 331 | |
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[a4fee13] | 332 | template <bool IsBigEndian> |
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[00587dc] | 333 | struct RankHeader { |
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[a4fee13] | 334 | endian_specific_value<uint64_t, IsBigEndian> Coords[3]; |
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| 335 | endian_specific_value<uint64_t, IsBigEndian> NElems; |
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| 336 | endian_specific_value<uint64_t, IsBigEndian> Start; |
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| 337 | endian_specific_value<uint64_t, IsBigEndian> GlobalRank; |
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| 338 | }; |
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[00587dc] | 339 | |
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| 340 | static const size_t FilterNameSize = 8; |
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| 341 | static const size_t MaxFilters = 4; |
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[a4fee13] | 342 | template <bool IsBigEndian> |
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[00587dc] | 343 | struct BlockHeader { |
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| 344 | char Filters[MaxFilters][FilterNameSize]; |
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[a4fee13] | 345 | endian_specific_value<uint64_t, IsBigEndian> Start; |
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| 346 | endian_specific_value<uint64_t, IsBigEndian> Size; |
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| 347 | }; |
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[00587dc] | 348 | |
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[a4fee13] | 349 | template <bool IsBigEndian> |
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[00587dc] | 350 | struct CompressHeader { |
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[a4fee13] | 351 | endian_specific_value<uint64_t, IsBigEndian> OrigCRC; |
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| 352 | }; |
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[00587dc] | 353 | const char *CompressName = "BLOSC"; |
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| 354 | |
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[6461f57] | 355 | const char *LossyCompressName = "SZ"; |
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| 356 | |
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[a4fee13] | 357 | #pragma pack() |
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| 358 | |
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[00587dc] | 359 | unsigned GenericIO::DefaultFileIOType = FileIOPOSIX; |
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| 360 | int GenericIO::DefaultPartition = 0; |
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| 361 | bool GenericIO::DefaultShouldCompress = false; |
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| 362 | |
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| 363 | #ifndef GENERICIO_NO_MPI |
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| 364 | std::size_t GenericIO::CollectiveMPIIOThreshold = 0; |
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| 365 | #endif |
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| 366 | |
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| 367 | static bool blosc_initialized = false; |
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[6461f57] | 368 | static bool sz_initialized = false; |
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[00587dc] | 369 | |
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| 370 | #ifndef GENERICIO_NO_MPI |
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[a4fee13] | 371 | void GenericIO::write() { |
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| 372 | if (isBigEndian()) |
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| 373 | write<true>(); |
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| 374 | else |
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| 375 | write<false>(); |
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| 376 | } |
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| 377 | |
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[00587dc] | 378 | // Note: writing errors are not currently recoverable (one rank may fail |
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| 379 | // while the others don't). |
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[a4fee13] | 380 | template <bool IsBigEndian> |
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[00587dc] | 381 | void GenericIO::write() { |
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[a4fee13] | 382 | const char *Magic = IsBigEndian ? MagicBE : MagicLE; |
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[00587dc] | 383 | |
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| 384 | uint64_t FileSize = 0; |
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| 385 | |
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| 386 | int NRanks, Rank; |
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| 387 | MPI_Comm_rank(Comm, &Rank); |
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| 388 | MPI_Comm_size(Comm, &NRanks); |
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| 389 | |
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| 390 | #ifdef __bgq__ |
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| 391 | MPI_Barrier(Comm); |
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| 392 | #endif |
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| 393 | MPI_Comm_split(Comm, Partition, Rank, &SplitComm); |
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| 394 | |
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| 395 | int SplitNRanks, SplitRank; |
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| 396 | MPI_Comm_rank(SplitComm, &SplitRank); |
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| 397 | MPI_Comm_size(SplitComm, &SplitNRanks); |
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| 398 | |
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| 399 | string LocalFileName; |
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| 400 | if (SplitNRanks != NRanks) { |
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| 401 | if (Rank == 0) { |
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| 402 | // In split mode, the specified file becomes the rank map, and the real |
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| 403 | // data is partitioned. |
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| 404 | |
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| 405 | vector<int> MapRank, MapPartition; |
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| 406 | MapRank.resize(NRanks); |
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| 407 | for (int i = 0; i < NRanks; ++i) MapRank[i] = i; |
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| 408 | |
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| 409 | MapPartition.resize(NRanks); |
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| 410 | MPI_Gather(&Partition, 1, MPI_INT, &MapPartition[0], 1, MPI_INT, 0, Comm); |
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| 411 | |
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| 412 | GenericIO GIO(MPI_COMM_SELF, FileName, FileIOType); |
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| 413 | GIO.setNumElems(NRanks); |
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| 414 | GIO.addVariable("$rank", MapRank); /* this is for use by humans; the reading |
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| 415 | code assumes that the partitions are in |
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| 416 | rank order */ |
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| 417 | GIO.addVariable("$partition", MapPartition); |
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| 418 | |
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| 419 | vector<int> CX, CY, CZ; |
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| 420 | int TopoStatus; |
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| 421 | MPI_Topo_test(Comm, &TopoStatus); |
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| 422 | if (TopoStatus == MPI_CART) { |
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| 423 | CX.resize(NRanks); |
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| 424 | CY.resize(NRanks); |
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| 425 | CZ.resize(NRanks); |
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| 426 | |
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| 427 | for (int i = 0; i < NRanks; ++i) { |
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| 428 | int C[3]; |
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| 429 | MPI_Cart_coords(Comm, i, 3, C); |
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| 430 | |
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| 431 | CX[i] = C[0]; |
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| 432 | CY[i] = C[1]; |
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| 433 | CZ[i] = C[2]; |
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| 434 | } |
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| 435 | |
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| 436 | GIO.addVariable("$x", CX); |
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| 437 | GIO.addVariable("$y", CY); |
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| 438 | GIO.addVariable("$z", CZ); |
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| 439 | } |
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| 440 | |
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| 441 | GIO.write(); |
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| 442 | } else { |
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| 443 | MPI_Gather(&Partition, 1, MPI_INT, 0, 0, MPI_INT, 0, Comm); |
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| 444 | } |
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| 445 | |
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| 446 | stringstream ss; |
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| 447 | ss << FileName << "#" << Partition; |
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| 448 | LocalFileName = ss.str(); |
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| 449 | } else { |
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| 450 | LocalFileName = FileName; |
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| 451 | } |
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| 452 | |
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[a4fee13] | 453 | RankHeader<IsBigEndian> RHLocal; |
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[00587dc] | 454 | int Dims[3], Periods[3], Coords[3]; |
---|
| 455 | |
---|
| 456 | int TopoStatus; |
---|
| 457 | MPI_Topo_test(Comm, &TopoStatus); |
---|
| 458 | if (TopoStatus == MPI_CART) { |
---|
| 459 | MPI_Cart_get(Comm, 3, Dims, Periods, Coords); |
---|
| 460 | } else { |
---|
| 461 | Dims[0] = NRanks; |
---|
| 462 | std::fill(Dims + 1, Dims + 3, 1); |
---|
| 463 | std::fill(Periods, Periods + 3, 0); |
---|
| 464 | Coords[0] = Rank; |
---|
| 465 | std::fill(Coords + 1, Coords + 3, 0); |
---|
| 466 | } |
---|
| 467 | |
---|
| 468 | std::copy(Coords, Coords + 3, RHLocal.Coords); |
---|
| 469 | RHLocal.NElems = NElems; |
---|
| 470 | RHLocal.Start = 0; |
---|
| 471 | RHLocal.GlobalRank = Rank; |
---|
| 472 | |
---|
| 473 | bool ShouldCompress = DefaultShouldCompress; |
---|
| 474 | const char *EnvStr = getenv("GENERICIO_COMPRESS"); |
---|
| 475 | if (EnvStr) { |
---|
| 476 | int Mod = atoi(EnvStr); |
---|
| 477 | ShouldCompress = (Mod > 0); |
---|
| 478 | } |
---|
| 479 | |
---|
| 480 | bool NeedsBlockHeaders = ShouldCompress; |
---|
| 481 | EnvStr = getenv("GENERICIO_FORCE_BLOCKS"); |
---|
| 482 | if (!NeedsBlockHeaders && EnvStr) { |
---|
| 483 | int Mod = atoi(EnvStr); |
---|
| 484 | NeedsBlockHeaders = (Mod > 0); |
---|
| 485 | } |
---|
| 486 | |
---|
[a4fee13] | 487 | vector<BlockHeader<IsBigEndian> > LocalBlockHeaders; |
---|
[00587dc] | 488 | vector<void *> LocalData; |
---|
| 489 | vector<bool> LocalHasExtraSpace; |
---|
| 490 | vector<vector<unsigned char> > LocalCData; |
---|
| 491 | if (NeedsBlockHeaders) { |
---|
| 492 | LocalBlockHeaders.resize(Vars.size()); |
---|
| 493 | LocalData.resize(Vars.size()); |
---|
| 494 | LocalHasExtraSpace.resize(Vars.size()); |
---|
| 495 | if (ShouldCompress) |
---|
| 496 | LocalCData.resize(Vars.size()); |
---|
| 497 | |
---|
| 498 | for (size_t i = 0; i < Vars.size(); ++i) { |
---|
| 499 | // Filters null by default, leave null starting address (needs to be |
---|
| 500 | // calculated by the header-writing rank). |
---|
[a4fee13] | 501 | memset(&LocalBlockHeaders[i], 0, sizeof(BlockHeader<IsBigEndian>)); |
---|
[00587dc] | 502 | if (ShouldCompress) { |
---|
[a4fee13] | 503 | LocalCData[i].resize(sizeof(CompressHeader<IsBigEndian>)); |
---|
[00587dc] | 504 | |
---|
[a4fee13] | 505 | CompressHeader<IsBigEndian> *CH = (CompressHeader<IsBigEndian>*) &LocalCData[i][0]; |
---|
[00587dc] | 506 | CH->OrigCRC = crc64_omp(Vars[i].Data, Vars[i].Size*NElems); |
---|
| 507 | |
---|
| 508 | #ifdef _OPENMP |
---|
| 509 | #pragma omp master |
---|
| 510 | { |
---|
| 511 | #endif |
---|
| 512 | |
---|
| 513 | if (!blosc_initialized) { |
---|
| 514 | blosc_init(); |
---|
| 515 | blosc_initialized = true; |
---|
| 516 | } |
---|
| 517 | |
---|
[2c47b73] | 518 | if (!sz_initialized) { |
---|
| 519 | SZ_Init(NULL); |
---|
| 520 | sz_initialized = true; |
---|
| 521 | } |
---|
| 522 | |
---|
[00587dc] | 523 | #ifdef _OPENMP |
---|
| 524 | blosc_set_nthreads(omp_get_max_threads()); |
---|
| 525 | } |
---|
| 526 | #endif |
---|
| 527 | |
---|
| 528 | LocalCData[i].resize(LocalCData[i].size() + NElems*Vars[i].Size); |
---|
| 529 | if (blosc_compress(9, 1, Vars[i].Size, NElems*Vars[i].Size, Vars[i].Data, |
---|
[a4fee13] | 530 | &LocalCData[i][0] + sizeof(CompressHeader<IsBigEndian>), |
---|
[00587dc] | 531 | NElems*Vars[i].Size) <= 0) |
---|
| 532 | goto nocomp; |
---|
| 533 | |
---|
| 534 | strncpy(LocalBlockHeaders[i].Filters[0], CompressName, FilterNameSize); |
---|
| 535 | size_t CNBytes, CCBytes, CBlockSize; |
---|
[a4fee13] | 536 | blosc_cbuffer_sizes(&LocalCData[i][0] + sizeof(CompressHeader<IsBigEndian>), |
---|
[00587dc] | 537 | &CNBytes, &CCBytes, &CBlockSize); |
---|
[a4fee13] | 538 | LocalCData[i].resize(CCBytes + sizeof(CompressHeader<IsBigEndian>)); |
---|
[00587dc] | 539 | |
---|
| 540 | LocalBlockHeaders[i].Size = LocalCData[i].size(); |
---|
| 541 | LocalCData[i].resize(LocalCData[i].size() + CRCSize); |
---|
| 542 | LocalData[i] = &LocalCData[i][0]; |
---|
| 543 | LocalHasExtraSpace[i] = true; |
---|
| 544 | } else { |
---|
| 545 | nocomp: |
---|
| 546 | LocalBlockHeaders[i].Size = NElems*Vars[i].Size; |
---|
| 547 | LocalData[i] = Vars[i].Data; |
---|
| 548 | LocalHasExtraSpace[i] = Vars[i].HasExtraSpace; |
---|
| 549 | } |
---|
| 550 | } |
---|
| 551 | } |
---|
| 552 | |
---|
| 553 | double StartTime = MPI_Wtime(); |
---|
| 554 | |
---|
| 555 | if (SplitRank == 0) { |
---|
[a4fee13] | 556 | uint64_t HeaderSize = sizeof(GlobalHeader<IsBigEndian>) + Vars.size()*sizeof(VariableHeader<IsBigEndian>) + |
---|
| 557 | SplitNRanks*sizeof(RankHeader<IsBigEndian>) + CRCSize; |
---|
[00587dc] | 558 | if (NeedsBlockHeaders) |
---|
[a4fee13] | 559 | HeaderSize += SplitNRanks*Vars.size()*sizeof(BlockHeader<IsBigEndian>); |
---|
[00587dc] | 560 | |
---|
| 561 | vector<char> Header(HeaderSize, 0); |
---|
[a4fee13] | 562 | GlobalHeader<IsBigEndian> *GH = (GlobalHeader<IsBigEndian> *) &Header[0]; |
---|
[00587dc] | 563 | std::copy(Magic, Magic + MagicSize, GH->Magic); |
---|
| 564 | GH->HeaderSize = HeaderSize - CRCSize; |
---|
| 565 | GH->NElems = NElems; // This will be updated later |
---|
| 566 | std::copy(Dims, Dims + 3, GH->Dims); |
---|
| 567 | GH->NVars = Vars.size(); |
---|
[a4fee13] | 568 | GH->VarsSize = sizeof(VariableHeader<IsBigEndian>); |
---|
| 569 | GH->VarsStart = sizeof(GlobalHeader<IsBigEndian>); |
---|
[00587dc] | 570 | GH->NRanks = SplitNRanks; |
---|
[a4fee13] | 571 | GH->RanksSize = sizeof(RankHeader<IsBigEndian>); |
---|
| 572 | GH->RanksStart = GH->VarsStart + Vars.size()*sizeof(VariableHeader<IsBigEndian>); |
---|
| 573 | GH->GlobalHeaderSize = sizeof(GlobalHeader<IsBigEndian>); |
---|
[00587dc] | 574 | std::copy(PhysOrigin, PhysOrigin + 3, GH->PhysOrigin); |
---|
| 575 | std::copy(PhysScale, PhysScale + 3, GH->PhysScale); |
---|
| 576 | if (!NeedsBlockHeaders) { |
---|
| 577 | GH->BlocksSize = GH->BlocksStart = 0; |
---|
| 578 | } else { |
---|
[a4fee13] | 579 | GH->BlocksSize = sizeof(BlockHeader<IsBigEndian>); |
---|
| 580 | GH->BlocksStart = GH->RanksStart + SplitNRanks*sizeof(RankHeader<IsBigEndian>); |
---|
[00587dc] | 581 | } |
---|
| 582 | |
---|
| 583 | uint64_t RecordSize = 0; |
---|
[a4fee13] | 584 | VariableHeader<IsBigEndian> *VH = (VariableHeader<IsBigEndian> *) &Header[GH->VarsStart]; |
---|
[00587dc] | 585 | for (size_t i = 0; i < Vars.size(); ++i, ++VH) { |
---|
| 586 | string VName(Vars[i].Name); |
---|
| 587 | VName.resize(NameSize); |
---|
| 588 | |
---|
| 589 | std::copy(VName.begin(), VName.end(), VH->Name); |
---|
[a4fee13] | 590 | uint64_t VFlags = 0; |
---|
| 591 | if (Vars[i].IsFloat) VFlags |= FloatValue; |
---|
| 592 | if (Vars[i].IsSigned) VFlags |= SignedValue; |
---|
| 593 | if (Vars[i].IsPhysCoordX) VFlags |= ValueIsPhysCoordX; |
---|
| 594 | if (Vars[i].IsPhysCoordY) VFlags |= ValueIsPhysCoordY; |
---|
| 595 | if (Vars[i].IsPhysCoordZ) VFlags |= ValueIsPhysCoordZ; |
---|
| 596 | if (Vars[i].MaybePhysGhost) VFlags |= ValueMaybePhysGhost; |
---|
| 597 | VH->Flags = VFlags; |
---|
[00587dc] | 598 | RecordSize += VH->Size = Vars[i].Size; |
---|
[5d57155] | 599 | VH->ElementSize = Vars[i].ElementSize; |
---|
[00587dc] | 600 | } |
---|
| 601 | |
---|
| 602 | MPI_Gather(&RHLocal, sizeof(RHLocal), MPI_BYTE, |
---|
| 603 | &Header[GH->RanksStart], sizeof(RHLocal), |
---|
| 604 | MPI_BYTE, 0, SplitComm); |
---|
| 605 | |
---|
| 606 | if (NeedsBlockHeaders) { |
---|
| 607 | MPI_Gather(&LocalBlockHeaders[0], |
---|
[a4fee13] | 608 | Vars.size()*sizeof(BlockHeader<IsBigEndian>), MPI_BYTE, |
---|
[00587dc] | 609 | &Header[GH->BlocksStart], |
---|
[a4fee13] | 610 | Vars.size()*sizeof(BlockHeader<IsBigEndian>), MPI_BYTE, |
---|
[00587dc] | 611 | 0, SplitComm); |
---|
| 612 | |
---|
[a4fee13] | 613 | BlockHeader<IsBigEndian> *BH = (BlockHeader<IsBigEndian> *) &Header[GH->BlocksStart]; |
---|
[00587dc] | 614 | for (int i = 0; i < SplitNRanks; ++i) |
---|
| 615 | for (size_t j = 0; j < Vars.size(); ++j, ++BH) { |
---|
| 616 | if (i == 0 && j == 0) |
---|
| 617 | BH->Start = HeaderSize; |
---|
| 618 | else |
---|
| 619 | BH->Start = BH[-1].Start + BH[-1].Size + CRCSize; |
---|
| 620 | } |
---|
| 621 | |
---|
[a4fee13] | 622 | RankHeader<IsBigEndian> *RH = (RankHeader<IsBigEndian> *) &Header[GH->RanksStart]; |
---|
[00587dc] | 623 | RH->Start = HeaderSize; ++RH; |
---|
| 624 | for (int i = 1; i < SplitNRanks; ++i, ++RH) { |
---|
| 625 | RH->Start = |
---|
[a4fee13] | 626 | ((BlockHeader<IsBigEndian> *) &Header[GH->BlocksStart])[i*Vars.size()].Start; |
---|
[00587dc] | 627 | GH->NElems += RH->NElems; |
---|
| 628 | } |
---|
| 629 | |
---|
| 630 | // Compute the total file size. |
---|
| 631 | uint64_t LastData = BH[-1].Size + CRCSize; |
---|
| 632 | FileSize = BH[-1].Start + LastData; |
---|
| 633 | } else { |
---|
[a4fee13] | 634 | RankHeader<IsBigEndian> *RH = (RankHeader<IsBigEndian> *) &Header[GH->RanksStart]; |
---|
[00587dc] | 635 | RH->Start = HeaderSize; ++RH; |
---|
| 636 | for (int i = 1; i < SplitNRanks; ++i, ++RH) { |
---|
| 637 | uint64_t PrevNElems = RH[-1].NElems; |
---|
| 638 | uint64_t PrevData = PrevNElems*RecordSize + CRCSize*Vars.size(); |
---|
| 639 | RH->Start = RH[-1].Start + PrevData; |
---|
| 640 | GH->NElems += RH->NElems; |
---|
| 641 | } |
---|
| 642 | |
---|
| 643 | // Compute the total file size. |
---|
| 644 | uint64_t LastNElems = RH[-1].NElems; |
---|
| 645 | uint64_t LastData = LastNElems*RecordSize + CRCSize*Vars.size(); |
---|
| 646 | FileSize = RH[-1].Start + LastData; |
---|
| 647 | } |
---|
| 648 | |
---|
| 649 | // Now that the starting offset has been computed, send it back to each rank. |
---|
| 650 | MPI_Scatter(&Header[GH->RanksStart], sizeof(RHLocal), |
---|
| 651 | MPI_BYTE, &RHLocal, sizeof(RHLocal), |
---|
| 652 | MPI_BYTE, 0, SplitComm); |
---|
| 653 | |
---|
| 654 | if (NeedsBlockHeaders) |
---|
| 655 | MPI_Scatter(&Header[GH->BlocksStart], |
---|
[a4fee13] | 656 | sizeof(BlockHeader<IsBigEndian>)*Vars.size(), MPI_BYTE, |
---|
[00587dc] | 657 | &LocalBlockHeaders[0], |
---|
[a4fee13] | 658 | sizeof(BlockHeader<IsBigEndian>)*Vars.size(), MPI_BYTE, |
---|
[00587dc] | 659 | 0, SplitComm); |
---|
| 660 | |
---|
| 661 | uint64_t HeaderCRC = crc64_omp(&Header[0], HeaderSize - CRCSize); |
---|
| 662 | crc64_invert(HeaderCRC, &Header[HeaderSize - CRCSize]); |
---|
| 663 | |
---|
| 664 | if (FileIOType == FileIOMPI) |
---|
| 665 | FH.get() = new GenericFileIO_MPI(MPI_COMM_SELF); |
---|
| 666 | else if (FileIOType == FileIOMPICollective) |
---|
| 667 | FH.get() = new GenericFileIO_MPICollective(MPI_COMM_SELF); |
---|
| 668 | else |
---|
| 669 | FH.get() = new GenericFileIO_POSIX(); |
---|
| 670 | |
---|
| 671 | FH.get()->open(LocalFileName); |
---|
| 672 | FH.get()->setSize(FileSize); |
---|
| 673 | FH.get()->write(&Header[0], HeaderSize, 0, "header"); |
---|
| 674 | |
---|
| 675 | close(); |
---|
| 676 | } else { |
---|
| 677 | MPI_Gather(&RHLocal, sizeof(RHLocal), MPI_BYTE, 0, 0, MPI_BYTE, 0, SplitComm); |
---|
| 678 | if (NeedsBlockHeaders) |
---|
[a4fee13] | 679 | MPI_Gather(&LocalBlockHeaders[0], Vars.size()*sizeof(BlockHeader<IsBigEndian>), |
---|
[00587dc] | 680 | MPI_BYTE, 0, 0, MPI_BYTE, 0, SplitComm); |
---|
| 681 | MPI_Scatter(0, 0, MPI_BYTE, &RHLocal, sizeof(RHLocal), MPI_BYTE, 0, SplitComm); |
---|
| 682 | if (NeedsBlockHeaders) |
---|
[a4fee13] | 683 | MPI_Scatter(0, 0, MPI_BYTE, &LocalBlockHeaders[0], sizeof(BlockHeader<IsBigEndian>)*Vars.size(), |
---|
[00587dc] | 684 | MPI_BYTE, 0, SplitComm); |
---|
| 685 | } |
---|
| 686 | |
---|
| 687 | MPI_Barrier(SplitComm); |
---|
| 688 | |
---|
| 689 | if (FileIOType == FileIOMPI) |
---|
| 690 | FH.get() = new GenericFileIO_MPI(SplitComm); |
---|
| 691 | else if (FileIOType == FileIOMPICollective) |
---|
| 692 | FH.get() = new GenericFileIO_MPICollective(SplitComm); |
---|
| 693 | else |
---|
| 694 | FH.get() = new GenericFileIO_POSIX(); |
---|
| 695 | |
---|
| 696 | FH.get()->open(LocalFileName); |
---|
| 697 | |
---|
| 698 | uint64_t Offset = RHLocal.Start; |
---|
| 699 | for (size_t i = 0; i < Vars.size(); ++i) { |
---|
| 700 | uint64_t WriteSize = NeedsBlockHeaders ? |
---|
| 701 | LocalBlockHeaders[i].Size : NElems*Vars[i].Size; |
---|
| 702 | void *Data = NeedsBlockHeaders ? LocalData[i] : Vars[i].Data; |
---|
| 703 | uint64_t CRC = crc64_omp(Data, WriteSize); |
---|
| 704 | bool HasExtraSpace = NeedsBlockHeaders ? |
---|
| 705 | LocalHasExtraSpace[i] : Vars[i].HasExtraSpace; |
---|
| 706 | char *CRCLoc = HasExtraSpace ? ((char *) Data) + WriteSize : (char *) &CRC; |
---|
| 707 | |
---|
| 708 | if (NeedsBlockHeaders) |
---|
| 709 | Offset = LocalBlockHeaders[i].Start; |
---|
| 710 | |
---|
| 711 | // When using extra space for the CRC write, preserve the original contents. |
---|
| 712 | char CRCSave[CRCSize]; |
---|
| 713 | if (HasExtraSpace) |
---|
| 714 | std::copy(CRCLoc, CRCLoc + CRCSize, CRCSave); |
---|
| 715 | |
---|
| 716 | crc64_invert(CRC, CRCLoc); |
---|
| 717 | |
---|
| 718 | if (HasExtraSpace) { |
---|
| 719 | FH.get()->write(Data, WriteSize + CRCSize, Offset, Vars[i].Name + " with CRC"); |
---|
| 720 | } else { |
---|
| 721 | FH.get()->write(Data, WriteSize, Offset, Vars[i].Name); |
---|
| 722 | FH.get()->write(CRCLoc, CRCSize, Offset + WriteSize, Vars[i].Name + " CRC"); |
---|
| 723 | } |
---|
| 724 | |
---|
| 725 | if (HasExtraSpace) |
---|
| 726 | std::copy(CRCSave, CRCSave + CRCSize, CRCLoc); |
---|
| 727 | |
---|
| 728 | Offset += WriteSize + CRCSize; |
---|
| 729 | } |
---|
| 730 | |
---|
| 731 | close(); |
---|
| 732 | MPI_Barrier(Comm); |
---|
| 733 | |
---|
| 734 | double EndTime = MPI_Wtime(); |
---|
| 735 | double TotalTime = EndTime - StartTime; |
---|
| 736 | double MaxTotalTime; |
---|
| 737 | MPI_Reduce(&TotalTime, &MaxTotalTime, 1, MPI_DOUBLE, MPI_MAX, 0, Comm); |
---|
| 738 | |
---|
| 739 | if (SplitNRanks != NRanks) { |
---|
| 740 | uint64_t ContribFileSize = (SplitRank == 0) ? FileSize : 0; |
---|
| 741 | MPI_Reduce(&ContribFileSize, &FileSize, 1, MPI_UINT64_T, MPI_SUM, 0, Comm); |
---|
| 742 | } |
---|
| 743 | |
---|
| 744 | if (Rank == 0) { |
---|
| 745 | double Rate = ((double) FileSize) / MaxTotalTime / (1024.*1024.); |
---|
[d6628a6] | 746 | std::cout << "Wrote " << Vars.size() << " variables to " << FileName << |
---|
| 747 | " (" << FileSize << " bytes) in " << MaxTotalTime << "s: " << |
---|
| 748 | Rate << " MB/s" << std::endl; |
---|
[00587dc] | 749 | } |
---|
| 750 | |
---|
| 751 | MPI_Comm_free(&SplitComm); |
---|
| 752 | SplitComm = MPI_COMM_NULL; |
---|
| 753 | } |
---|
| 754 | #endif // GENERICIO_NO_MPI |
---|
| 755 | |
---|
[a4fee13] | 756 | template <bool IsBigEndian> |
---|
[8f0a211] | 757 | void GenericIO::readHeaderLeader(void *GHPtr, MismatchBehavior MB, int NRanks, |
---|
| 758 | int Rank, int SplitNRanks, |
---|
| 759 | string &LocalFileName, uint64_t &HeaderSize, |
---|
| 760 | vector<char> &Header) { |
---|
[a4fee13] | 761 | GlobalHeader<IsBigEndian> &GH = *(GlobalHeader<IsBigEndian> *) GHPtr; |
---|
| 762 | |
---|
[8f0a211] | 763 | if (MB == MismatchDisallowed) { |
---|
[a4fee13] | 764 | if (SplitNRanks != (int) GH.NRanks) { |
---|
| 765 | stringstream ss; |
---|
| 766 | ss << "Won't read " << LocalFileName << ": communicator-size mismatch: " << |
---|
| 767 | "current: " << SplitNRanks << ", file: " << GH.NRanks; |
---|
| 768 | throw runtime_error(ss.str()); |
---|
| 769 | } |
---|
| 770 | |
---|
| 771 | #ifndef GENERICIO_NO_MPI |
---|
| 772 | int TopoStatus; |
---|
| 773 | MPI_Topo_test(Comm, &TopoStatus); |
---|
| 774 | if (TopoStatus == MPI_CART) { |
---|
| 775 | int Dims[3], Periods[3], Coords[3]; |
---|
| 776 | MPI_Cart_get(Comm, 3, Dims, Periods, Coords); |
---|
| 777 | |
---|
| 778 | bool DimsMatch = true; |
---|
| 779 | for (int i = 0; i < 3; ++i) { |
---|
| 780 | if ((uint64_t) Dims[i] != GH.Dims[i]) { |
---|
| 781 | DimsMatch = false; |
---|
| 782 | break; |
---|
| 783 | } |
---|
| 784 | } |
---|
| 785 | |
---|
| 786 | if (!DimsMatch) { |
---|
| 787 | stringstream ss; |
---|
| 788 | ss << "Won't read " << LocalFileName << |
---|
| 789 | ": communicator-decomposition mismatch: " << |
---|
| 790 | "current: " << Dims[0] << "x" << Dims[1] << "x" << Dims[2] << |
---|
| 791 | ", file: " << GH.Dims[0] << "x" << GH.Dims[1] << "x" << |
---|
| 792 | GH.Dims[2]; |
---|
| 793 | throw runtime_error(ss.str()); |
---|
| 794 | } |
---|
| 795 | } |
---|
| 796 | #endif |
---|
[8f0a211] | 797 | } else if (MB == MismatchRedistribute && !Redistributing) { |
---|
| 798 | Redistributing = true; |
---|
| 799 | |
---|
| 800 | int NFileRanks = RankMap.empty() ? (int) GH.NRanks : (int) RankMap.size(); |
---|
| 801 | int NFileRanksPerRank = NFileRanks/NRanks; |
---|
| 802 | int NRemFileRank = NFileRanks % NRanks; |
---|
| 803 | |
---|
| 804 | if (!NFileRanksPerRank) { |
---|
| 805 | // We have only the remainder, so the last NRemFileRank ranks get one |
---|
| 806 | // file rank, and the others don't. |
---|
| 807 | if (NRemFileRank && NRanks - Rank <= NRemFileRank) |
---|
| 808 | SourceRanks.push_back(NRanks - (Rank + 1)); |
---|
| 809 | } else { |
---|
| 810 | // Since NRemFileRank < NRanks, and we don't want to put any extra memory |
---|
| 811 | // load on rank 0 (because rank 0's memory load is normally higher than |
---|
| 812 | // the other ranks anyway), the last NRemFileRank will each take |
---|
| 813 | // (NFileRanksPerRank+1) file ranks. |
---|
| 814 | |
---|
| 815 | int FirstFileRank = 0, LastFileRank = NFileRanksPerRank - 1; |
---|
| 816 | for (int i = 1; i <= Rank; ++i) { |
---|
| 817 | FirstFileRank = LastFileRank + 1; |
---|
| 818 | LastFileRank = FirstFileRank + NFileRanksPerRank - 1; |
---|
| 819 | |
---|
| 820 | if (NRemFileRank && NRanks - i <= NRemFileRank) |
---|
| 821 | ++LastFileRank; |
---|
| 822 | } |
---|
| 823 | |
---|
| 824 | for (int i = FirstFileRank; i <= LastFileRank; ++i) |
---|
| 825 | SourceRanks.push_back(i); |
---|
| 826 | } |
---|
[a4fee13] | 827 | } |
---|
| 828 | |
---|
| 829 | HeaderSize = GH.HeaderSize; |
---|
| 830 | Header.resize(HeaderSize + CRCSize, 0xFE /* poison */); |
---|
| 831 | FH.get()->read(&Header[0], HeaderSize + CRCSize, 0, "header"); |
---|
| 832 | |
---|
| 833 | uint64_t CRC = crc64_omp(&Header[0], HeaderSize + CRCSize); |
---|
| 834 | if (CRC != (uint64_t) -1) { |
---|
| 835 | throw runtime_error("Header CRC check failed: " + LocalFileName); |
---|
| 836 | } |
---|
| 837 | } |
---|
| 838 | |
---|
[00587dc] | 839 | // Note: Errors from this function should be recoverable. This means that if |
---|
| 840 | // one rank throws an exception, then all ranks should. |
---|
[8f0a211] | 841 | void GenericIO::openAndReadHeader(MismatchBehavior MB, int EffRank, bool CheckPartMap) { |
---|
[00587dc] | 842 | int NRanks, Rank; |
---|
| 843 | #ifndef GENERICIO_NO_MPI |
---|
| 844 | MPI_Comm_rank(Comm, &Rank); |
---|
| 845 | MPI_Comm_size(Comm, &NRanks); |
---|
| 846 | #else |
---|
| 847 | Rank = 0; |
---|
| 848 | NRanks = 1; |
---|
| 849 | #endif |
---|
| 850 | |
---|
| 851 | if (EffRank == -1) |
---|
[8f0a211] | 852 | EffRank = MB == MismatchRedistribute ? 0 : Rank; |
---|
[00587dc] | 853 | |
---|
| 854 | if (RankMap.empty() && CheckPartMap) { |
---|
| 855 | // First, check to see if the file is a rank map. |
---|
| 856 | unsigned long RanksInMap = 0; |
---|
| 857 | if (Rank == 0) { |
---|
| 858 | try { |
---|
| 859 | #ifndef GENERICIO_NO_MPI |
---|
| 860 | GenericIO GIO(MPI_COMM_SELF, FileName, FileIOType); |
---|
| 861 | #else |
---|
| 862 | GenericIO GIO(FileName, FileIOType); |
---|
| 863 | #endif |
---|
[8f0a211] | 864 | GIO.openAndReadHeader(MismatchDisallowed, 0, false); |
---|
[00587dc] | 865 | RanksInMap = GIO.readNumElems(); |
---|
| 866 | |
---|
| 867 | RankMap.resize(RanksInMap + GIO.requestedExtraSpace()/sizeof(int)); |
---|
| 868 | GIO.addVariable("$partition", RankMap, true); |
---|
| 869 | |
---|
| 870 | GIO.readData(0, false); |
---|
| 871 | RankMap.resize(RanksInMap); |
---|
| 872 | } catch (...) { |
---|
| 873 | RankMap.clear(); |
---|
| 874 | RanksInMap = 0; |
---|
| 875 | } |
---|
| 876 | } |
---|
| 877 | |
---|
| 878 | #ifndef GENERICIO_NO_MPI |
---|
| 879 | MPI_Bcast(&RanksInMap, 1, MPI_UNSIGNED_LONG, 0, Comm); |
---|
| 880 | if (RanksInMap > 0) { |
---|
| 881 | RankMap.resize(RanksInMap); |
---|
| 882 | MPI_Bcast(&RankMap[0], RanksInMap, MPI_INT, 0, Comm); |
---|
| 883 | } |
---|
| 884 | #endif |
---|
| 885 | } |
---|
| 886 | |
---|
| 887 | #ifndef GENERICIO_NO_MPI |
---|
| 888 | if (SplitComm != MPI_COMM_NULL) |
---|
| 889 | MPI_Comm_free(&SplitComm); |
---|
| 890 | #endif |
---|
| 891 | |
---|
| 892 | string LocalFileName; |
---|
| 893 | if (RankMap.empty()) { |
---|
| 894 | LocalFileName = FileName; |
---|
| 895 | #ifndef GENERICIO_NO_MPI |
---|
[8f0a211] | 896 | MPI_Comm_dup(MB == MismatchRedistribute ? MPI_COMM_SELF : Comm, &SplitComm); |
---|
[00587dc] | 897 | #endif |
---|
| 898 | } else { |
---|
| 899 | stringstream ss; |
---|
| 900 | ss << FileName << "#" << RankMap[EffRank]; |
---|
| 901 | LocalFileName = ss.str(); |
---|
| 902 | #ifndef GENERICIO_NO_MPI |
---|
[8f0a211] | 903 | if (MB == MismatchRedistribute) { |
---|
| 904 | MPI_Comm_dup(MPI_COMM_SELF, &SplitComm); |
---|
| 905 | } else { |
---|
[00587dc] | 906 | #ifdef __bgq__ |
---|
[8f0a211] | 907 | MPI_Barrier(Comm); |
---|
[00587dc] | 908 | #endif |
---|
[8f0a211] | 909 | MPI_Comm_split(Comm, RankMap[EffRank], Rank, &SplitComm); |
---|
| 910 | } |
---|
[00587dc] | 911 | #endif |
---|
| 912 | } |
---|
| 913 | |
---|
| 914 | if (LocalFileName == OpenFileName) |
---|
| 915 | return; |
---|
| 916 | FH.close(); |
---|
| 917 | |
---|
| 918 | int SplitNRanks, SplitRank; |
---|
| 919 | #ifndef GENERICIO_NO_MPI |
---|
| 920 | MPI_Comm_rank(SplitComm, &SplitRank); |
---|
| 921 | MPI_Comm_size(SplitComm, &SplitNRanks); |
---|
| 922 | #else |
---|
| 923 | SplitRank = 0; |
---|
| 924 | SplitNRanks = 1; |
---|
| 925 | #endif |
---|
| 926 | |
---|
| 927 | uint64_t HeaderSize; |
---|
| 928 | vector<char> Header; |
---|
| 929 | |
---|
| 930 | if (SplitRank == 0) { |
---|
| 931 | #ifndef GENERICIO_NO_MPI |
---|
| 932 | if (FileIOType == FileIOMPI) |
---|
| 933 | FH.get() = new GenericFileIO_MPI(MPI_COMM_SELF); |
---|
| 934 | else if (FileIOType == FileIOMPICollective) |
---|
| 935 | FH.get() = new GenericFileIO_MPICollective(MPI_COMM_SELF); |
---|
| 936 | else |
---|
| 937 | #endif |
---|
| 938 | FH.get() = new GenericFileIO_POSIX(); |
---|
| 939 | |
---|
| 940 | #ifndef GENERICIO_NO_MPI |
---|
| 941 | char True = 1, False = 0; |
---|
| 942 | #endif |
---|
| 943 | |
---|
| 944 | try { |
---|
| 945 | FH.get()->open(LocalFileName, true); |
---|
| 946 | |
---|
[a4fee13] | 947 | GlobalHeader<false> GH; // endianness does not matter yet... |
---|
| 948 | FH.get()->read(&GH, sizeof(GlobalHeader<false>), 0, "global header"); |
---|
[00587dc] | 949 | |
---|
[a4fee13] | 950 | if (string(GH.Magic, GH.Magic + MagicSize - 1) == MagicLE) { |
---|
[8f0a211] | 951 | readHeaderLeader<false>(&GH, MB, NRanks, Rank, SplitNRanks, LocalFileName, |
---|
[a4fee13] | 952 | HeaderSize, Header); |
---|
| 953 | } else if (string(GH.Magic, GH.Magic + MagicSize - 1) == MagicBE) { |
---|
[8f0a211] | 954 | readHeaderLeader<true>(&GH, MB, NRanks, Rank, SplitNRanks, LocalFileName, |
---|
[a4fee13] | 955 | HeaderSize, Header); |
---|
| 956 | } else { |
---|
| 957 | string Error = "invalid file-type identifier"; |
---|
[00587dc] | 958 | throw runtime_error("Won't read " + LocalFileName + ": " + Error); |
---|
| 959 | } |
---|
| 960 | |
---|
| 961 | #ifndef GENERICIO_NO_MPI |
---|
| 962 | close(); |
---|
| 963 | MPI_Bcast(&True, 1, MPI_BYTE, 0, SplitComm); |
---|
| 964 | #endif |
---|
| 965 | } catch (...) { |
---|
| 966 | #ifndef GENERICIO_NO_MPI |
---|
| 967 | MPI_Bcast(&False, 1, MPI_BYTE, 0, SplitComm); |
---|
| 968 | #endif |
---|
| 969 | close(); |
---|
| 970 | throw; |
---|
| 971 | } |
---|
| 972 | } else { |
---|
| 973 | #ifndef GENERICIO_NO_MPI |
---|
| 974 | char Okay; |
---|
| 975 | MPI_Bcast(&Okay, 1, MPI_BYTE, 0, SplitComm); |
---|
| 976 | if (!Okay) |
---|
| 977 | throw runtime_error("Failure broadcast from rank 0"); |
---|
| 978 | #endif |
---|
| 979 | } |
---|
| 980 | |
---|
| 981 | #ifndef GENERICIO_NO_MPI |
---|
| 982 | MPI_Bcast(&HeaderSize, 1, MPI_UINT64_T, 0, SplitComm); |
---|
| 983 | #endif |
---|
| 984 | |
---|
| 985 | Header.resize(HeaderSize, 0xFD /* poison */); |
---|
| 986 | #ifndef GENERICIO_NO_MPI |
---|
| 987 | MPI_Bcast(&Header[0], HeaderSize, MPI_BYTE, 0, SplitComm); |
---|
| 988 | #endif |
---|
| 989 | |
---|
| 990 | FH.getHeaderCache().clear(); |
---|
[a4fee13] | 991 | |
---|
| 992 | GlobalHeader<false> *GH = (GlobalHeader<false> *) &Header[0]; |
---|
| 993 | FH.setIsBigEndian(string(GH->Magic, GH->Magic + MagicSize - 1) == MagicBE); |
---|
| 994 | |
---|
[00587dc] | 995 | FH.getHeaderCache().swap(Header); |
---|
| 996 | OpenFileName = LocalFileName; |
---|
| 997 | |
---|
| 998 | #ifndef GENERICIO_NO_MPI |
---|
[8f0a211] | 999 | if (!DisableCollErrChecking) |
---|
| 1000 | MPI_Barrier(Comm); |
---|
[00587dc] | 1001 | |
---|
| 1002 | if (FileIOType == FileIOMPI) |
---|
| 1003 | FH.get() = new GenericFileIO_MPI(SplitComm); |
---|
| 1004 | else if (FileIOType == FileIOMPICollective) |
---|
| 1005 | FH.get() = new GenericFileIO_MPICollective(SplitComm); |
---|
| 1006 | else |
---|
| 1007 | FH.get() = new GenericFileIO_POSIX(); |
---|
| 1008 | |
---|
| 1009 | int OpenErr = 0, TotOpenErr; |
---|
| 1010 | try { |
---|
| 1011 | FH.get()->open(LocalFileName, true); |
---|
[8f0a211] | 1012 | MPI_Allreduce(&OpenErr, &TotOpenErr, 1, MPI_INT, MPI_SUM, |
---|
| 1013 | DisableCollErrChecking ? MPI_COMM_SELF : Comm); |
---|
[00587dc] | 1014 | } catch (...) { |
---|
| 1015 | OpenErr = 1; |
---|
[8f0a211] | 1016 | MPI_Allreduce(&OpenErr, &TotOpenErr, 1, MPI_INT, MPI_SUM, |
---|
| 1017 | DisableCollErrChecking ? MPI_COMM_SELF : Comm); |
---|
[00587dc] | 1018 | throw; |
---|
| 1019 | } |
---|
| 1020 | |
---|
| 1021 | if (TotOpenErr > 0) { |
---|
| 1022 | stringstream ss; |
---|
| 1023 | ss << TotOpenErr << " ranks failed to open file: " << LocalFileName; |
---|
| 1024 | throw runtime_error(ss.str()); |
---|
| 1025 | } |
---|
| 1026 | #endif |
---|
| 1027 | } |
---|
| 1028 | |
---|
| 1029 | int GenericIO::readNRanks() { |
---|
[a4fee13] | 1030 | if (FH.isBigEndian()) |
---|
| 1031 | return readNRanks<true>(); |
---|
| 1032 | return readNRanks<false>(); |
---|
| 1033 | } |
---|
| 1034 | |
---|
| 1035 | template <bool IsBigEndian> |
---|
| 1036 | int GenericIO::readNRanks() { |
---|
[00587dc] | 1037 | if (RankMap.size()) |
---|
| 1038 | return RankMap.size(); |
---|
| 1039 | |
---|
| 1040 | assert(FH.getHeaderCache().size() && "HeaderCache must not be empty"); |
---|
[a4fee13] | 1041 | GlobalHeader<IsBigEndian> *GH = (GlobalHeader<IsBigEndian> *) &FH.getHeaderCache()[0]; |
---|
[00587dc] | 1042 | return (int) GH->NRanks; |
---|
| 1043 | } |
---|
| 1044 | |
---|
| 1045 | void GenericIO::readDims(int Dims[3]) { |
---|
[a4fee13] | 1046 | if (FH.isBigEndian()) |
---|
| 1047 | readDims<true>(Dims); |
---|
| 1048 | else |
---|
| 1049 | readDims<false>(Dims); |
---|
| 1050 | } |
---|
| 1051 | |
---|
| 1052 | template <bool IsBigEndian> |
---|
| 1053 | void GenericIO::readDims(int Dims[3]) { |
---|
[00587dc] | 1054 | assert(FH.getHeaderCache().size() && "HeaderCache must not be empty"); |
---|
[a4fee13] | 1055 | GlobalHeader<IsBigEndian> *GH = (GlobalHeader<IsBigEndian> *) &FH.getHeaderCache()[0]; |
---|
[00587dc] | 1056 | std::copy(GH->Dims, GH->Dims + 3, Dims); |
---|
| 1057 | } |
---|
| 1058 | |
---|
| 1059 | uint64_t GenericIO::readTotalNumElems() { |
---|
[a4fee13] | 1060 | if (FH.isBigEndian()) |
---|
| 1061 | return readTotalNumElems<true>(); |
---|
| 1062 | return readTotalNumElems<false>(); |
---|
| 1063 | } |
---|
| 1064 | |
---|
| 1065 | template <bool IsBigEndian> |
---|
| 1066 | uint64_t GenericIO::readTotalNumElems() { |
---|
[00587dc] | 1067 | if (RankMap.size()) |
---|
| 1068 | return (uint64_t) -1; |
---|
| 1069 | |
---|
| 1070 | assert(FH.getHeaderCache().size() && "HeaderCache must not be empty"); |
---|
[a4fee13] | 1071 | GlobalHeader<IsBigEndian> *GH = (GlobalHeader<IsBigEndian> *) &FH.getHeaderCache()[0]; |
---|
[00587dc] | 1072 | return GH->NElems; |
---|
| 1073 | } |
---|
| 1074 | |
---|
| 1075 | void GenericIO::readPhysOrigin(double Origin[3]) { |
---|
[a4fee13] | 1076 | if (FH.isBigEndian()) |
---|
| 1077 | readPhysOrigin<true>(Origin); |
---|
| 1078 | else |
---|
| 1079 | readPhysOrigin<false>(Origin); |
---|
| 1080 | } |
---|
| 1081 | |
---|
| 1082 | // Define a "safe" version of offsetof (offsetof itself might not work for |
---|
| 1083 | // non-POD types, and at least xlC v12.1 will complain about this if you try). |
---|
| 1084 | #define offsetof_safe(S, F) (size_t(&(S)->F) - size_t(S)) |
---|
| 1085 | |
---|
| 1086 | template <bool IsBigEndian> |
---|
| 1087 | void GenericIO::readPhysOrigin(double Origin[3]) { |
---|
[00587dc] | 1088 | assert(FH.getHeaderCache().size() && "HeaderCache must not be empty"); |
---|
[a4fee13] | 1089 | GlobalHeader<IsBigEndian> *GH = (GlobalHeader<IsBigEndian> *) &FH.getHeaderCache()[0]; |
---|
| 1090 | if (offsetof_safe(GH, PhysOrigin) >= GH->GlobalHeaderSize) { |
---|
[00587dc] | 1091 | std::fill(Origin, Origin + 3, 0.0); |
---|
| 1092 | return; |
---|
| 1093 | } |
---|
| 1094 | |
---|
| 1095 | std::copy(GH->PhysOrigin, GH->PhysOrigin + 3, Origin); |
---|
| 1096 | } |
---|
| 1097 | |
---|
| 1098 | void GenericIO::readPhysScale(double Scale[3]) { |
---|
[a4fee13] | 1099 | if (FH.isBigEndian()) |
---|
| 1100 | readPhysScale<true>(Scale); |
---|
| 1101 | else |
---|
| 1102 | readPhysScale<false>(Scale); |
---|
| 1103 | } |
---|
| 1104 | |
---|
| 1105 | template <bool IsBigEndian> |
---|
| 1106 | void GenericIO::readPhysScale(double Scale[3]) { |
---|
[00587dc] | 1107 | assert(FH.getHeaderCache().size() && "HeaderCache must not be empty"); |
---|
[a4fee13] | 1108 | GlobalHeader<IsBigEndian> *GH = (GlobalHeader<IsBigEndian> *) &FH.getHeaderCache()[0]; |
---|
| 1109 | if (offsetof_safe(GH, PhysScale) >= GH->GlobalHeaderSize) { |
---|
[00587dc] | 1110 | std::fill(Scale, Scale + 3, 0.0); |
---|
| 1111 | return; |
---|
| 1112 | } |
---|
| 1113 | |
---|
| 1114 | std::copy(GH->PhysScale, GH->PhysScale + 3, Scale); |
---|
| 1115 | } |
---|
| 1116 | |
---|
[a4fee13] | 1117 | template <bool IsBigEndian> |
---|
| 1118 | static size_t getRankIndex(int EffRank, GlobalHeader<IsBigEndian> *GH, |
---|
[00587dc] | 1119 | vector<int> &RankMap, vector<char> &HeaderCache) { |
---|
[a4fee13] | 1120 | if (RankMap.empty()) |
---|
[00587dc] | 1121 | return EffRank; |
---|
| 1122 | |
---|
| 1123 | for (size_t i = 0; i < GH->NRanks; ++i) { |
---|
[a4fee13] | 1124 | RankHeader<IsBigEndian> *RH = (RankHeader<IsBigEndian> *) &HeaderCache[GH->RanksStart + |
---|
[00587dc] | 1125 | i*GH->RanksSize]; |
---|
[a4fee13] | 1126 | if (offsetof_safe(RH, GlobalRank) >= GH->RanksSize) |
---|
| 1127 | return EffRank; |
---|
| 1128 | |
---|
[00587dc] | 1129 | if ((int) RH->GlobalRank == EffRank) |
---|
| 1130 | return i; |
---|
| 1131 | } |
---|
| 1132 | |
---|
| 1133 | assert(false && "Index requested of an invalid rank"); |
---|
| 1134 | return (size_t) -1; |
---|
| 1135 | } |
---|
| 1136 | |
---|
| 1137 | int GenericIO::readGlobalRankNumber(int EffRank) { |
---|
[a4fee13] | 1138 | if (FH.isBigEndian()) |
---|
| 1139 | return readGlobalRankNumber<true>(EffRank); |
---|
| 1140 | return readGlobalRankNumber<false>(EffRank); |
---|
| 1141 | } |
---|
| 1142 | |
---|
| 1143 | template <bool IsBigEndian> |
---|
| 1144 | int GenericIO::readGlobalRankNumber(int EffRank) { |
---|
[00587dc] | 1145 | if (EffRank == -1) { |
---|
| 1146 | #ifndef GENERICIO_NO_MPI |
---|
| 1147 | MPI_Comm_rank(Comm, &EffRank); |
---|
| 1148 | #else |
---|
| 1149 | EffRank = 0; |
---|
| 1150 | #endif |
---|
| 1151 | } |
---|
| 1152 | |
---|
[8f0a211] | 1153 | openAndReadHeader(MismatchAllowed, EffRank, false); |
---|
[00587dc] | 1154 | |
---|
| 1155 | assert(FH.getHeaderCache().size() && "HeaderCache must not be empty"); |
---|
| 1156 | |
---|
[a4fee13] | 1157 | GlobalHeader<IsBigEndian> *GH = (GlobalHeader<IsBigEndian> *) &FH.getHeaderCache()[0]; |
---|
| 1158 | size_t RankIndex = getRankIndex<IsBigEndian>(EffRank, GH, RankMap, FH.getHeaderCache()); |
---|
[00587dc] | 1159 | |
---|
| 1160 | assert(RankIndex < GH->NRanks && "Invalid rank specified"); |
---|
| 1161 | |
---|
[a4fee13] | 1162 | RankHeader<IsBigEndian> *RH = (RankHeader<IsBigEndian> *) &FH.getHeaderCache()[GH->RanksStart + |
---|
[00587dc] | 1163 | RankIndex*GH->RanksSize]; |
---|
| 1164 | |
---|
[a4fee13] | 1165 | if (offsetof_safe(RH, GlobalRank) >= GH->RanksSize) |
---|
| 1166 | return EffRank; |
---|
| 1167 | |
---|
[00587dc] | 1168 | return (int) RH->GlobalRank; |
---|
| 1169 | } |
---|
| 1170 | |
---|
[14e73bb] | 1171 | void GenericIO::getSourceRanks(vector<int> &SR) { |
---|
| 1172 | SR.clear(); |
---|
| 1173 | |
---|
| 1174 | if (Redistributing) { |
---|
| 1175 | std::copy(SourceRanks.begin(), SourceRanks.end(), std::back_inserter(SR)); |
---|
| 1176 | return; |
---|
| 1177 | } |
---|
| 1178 | |
---|
| 1179 | int Rank; |
---|
| 1180 | #ifndef GENERICIO_NO_MPI |
---|
| 1181 | MPI_Comm_rank(Comm, &Rank); |
---|
| 1182 | #else |
---|
| 1183 | Rank = 0; |
---|
| 1184 | #endif |
---|
| 1185 | |
---|
| 1186 | SR.push_back(Rank); |
---|
| 1187 | } |
---|
| 1188 | |
---|
[00587dc] | 1189 | size_t GenericIO::readNumElems(int EffRank) { |
---|
[8f0a211] | 1190 | if (EffRank == -1 && Redistributing) { |
---|
| 1191 | DisableCollErrChecking = true; |
---|
| 1192 | |
---|
| 1193 | size_t TotalSize = 0; |
---|
| 1194 | for (int i = 0, ie = SourceRanks.size(); i != ie; ++i) |
---|
| 1195 | TotalSize += readNumElems(SourceRanks[i]); |
---|
| 1196 | |
---|
| 1197 | DisableCollErrChecking = false; |
---|
| 1198 | return TotalSize; |
---|
| 1199 | } |
---|
| 1200 | |
---|
[a4fee13] | 1201 | if (FH.isBigEndian()) |
---|
| 1202 | return readNumElems<true>(EffRank); |
---|
| 1203 | return readNumElems<false>(EffRank); |
---|
| 1204 | } |
---|
| 1205 | |
---|
| 1206 | template <bool IsBigEndian> |
---|
| 1207 | size_t GenericIO::readNumElems(int EffRank) { |
---|
[00587dc] | 1208 | if (EffRank == -1) { |
---|
| 1209 | #ifndef GENERICIO_NO_MPI |
---|
| 1210 | MPI_Comm_rank(Comm, &EffRank); |
---|
| 1211 | #else |
---|
| 1212 | EffRank = 0; |
---|
| 1213 | #endif |
---|
| 1214 | } |
---|
| 1215 | |
---|
[8f0a211] | 1216 | openAndReadHeader(Redistributing ? MismatchRedistribute : MismatchAllowed, |
---|
| 1217 | EffRank, false); |
---|
[00587dc] | 1218 | |
---|
| 1219 | assert(FH.getHeaderCache().size() && "HeaderCache must not be empty"); |
---|
| 1220 | |
---|
[a4fee13] | 1221 | GlobalHeader<IsBigEndian> *GH = (GlobalHeader<IsBigEndian> *) &FH.getHeaderCache()[0]; |
---|
| 1222 | size_t RankIndex = getRankIndex<IsBigEndian>(EffRank, GH, RankMap, FH.getHeaderCache()); |
---|
[00587dc] | 1223 | |
---|
| 1224 | assert(RankIndex < GH->NRanks && "Invalid rank specified"); |
---|
| 1225 | |
---|
[a4fee13] | 1226 | RankHeader<IsBigEndian> *RH = (RankHeader<IsBigEndian> *) &FH.getHeaderCache()[GH->RanksStart + |
---|
[00587dc] | 1227 | RankIndex*GH->RanksSize]; |
---|
| 1228 | return (size_t) RH->NElems; |
---|
| 1229 | } |
---|
| 1230 | |
---|
| 1231 | void GenericIO::readCoords(int Coords[3], int EffRank) { |
---|
[8f0a211] | 1232 | if (EffRank == -1 && Redistributing) { |
---|
| 1233 | std::fill(Coords, Coords + 3, 0); |
---|
| 1234 | return; |
---|
| 1235 | } |
---|
| 1236 | |
---|
[a4fee13] | 1237 | if (FH.isBigEndian()) |
---|
| 1238 | readCoords<true>(Coords, EffRank); |
---|
| 1239 | else |
---|
| 1240 | readCoords<false>(Coords, EffRank); |
---|
| 1241 | } |
---|
| 1242 | |
---|
| 1243 | template <bool IsBigEndian> |
---|
| 1244 | void GenericIO::readCoords(int Coords[3], int EffRank) { |
---|
[00587dc] | 1245 | if (EffRank == -1) { |
---|
| 1246 | #ifndef GENERICIO_NO_MPI |
---|
| 1247 | MPI_Comm_rank(Comm, &EffRank); |
---|
| 1248 | #else |
---|
| 1249 | EffRank = 0; |
---|
| 1250 | #endif |
---|
| 1251 | } |
---|
| 1252 | |
---|
[8f0a211] | 1253 | openAndReadHeader(MismatchAllowed, EffRank, false); |
---|
[00587dc] | 1254 | |
---|
| 1255 | assert(FH.getHeaderCache().size() && "HeaderCache must not be empty"); |
---|
| 1256 | |
---|
[a4fee13] | 1257 | GlobalHeader<IsBigEndian> *GH = (GlobalHeader<IsBigEndian> *) &FH.getHeaderCache()[0]; |
---|
| 1258 | size_t RankIndex = getRankIndex<IsBigEndian>(EffRank, GH, RankMap, FH.getHeaderCache()); |
---|
[00587dc] | 1259 | |
---|
| 1260 | assert(RankIndex < GH->NRanks && "Invalid rank specified"); |
---|
| 1261 | |
---|
[a4fee13] | 1262 | RankHeader<IsBigEndian> *RH = (RankHeader<IsBigEndian> *) &FH.getHeaderCache()[GH->RanksStart + |
---|
[00587dc] | 1263 | RankIndex*GH->RanksSize]; |
---|
| 1264 | |
---|
| 1265 | std::copy(RH->Coords, RH->Coords + 3, Coords); |
---|
| 1266 | } |
---|
| 1267 | |
---|
[a4fee13] | 1268 | void GenericIO::readData(int EffRank, bool PrintStats, bool CollStats) { |
---|
[00587dc] | 1269 | int Rank; |
---|
| 1270 | #ifndef GENERICIO_NO_MPI |
---|
| 1271 | MPI_Comm_rank(Comm, &Rank); |
---|
| 1272 | #else |
---|
| 1273 | Rank = 0; |
---|
| 1274 | #endif |
---|
| 1275 | |
---|
[8f0a211] | 1276 | uint64_t TotalReadSize = 0; |
---|
| 1277 | #ifndef GENERICIO_NO_MPI |
---|
| 1278 | double StartTime = MPI_Wtime(); |
---|
| 1279 | #else |
---|
| 1280 | double StartTime = double(clock())/CLOCKS_PER_SEC; |
---|
| 1281 | #endif |
---|
| 1282 | |
---|
| 1283 | int NErrs[3] = { 0, 0, 0 }; |
---|
| 1284 | |
---|
| 1285 | if (EffRank == -1 && Redistributing) { |
---|
| 1286 | DisableCollErrChecking = true; |
---|
| 1287 | |
---|
| 1288 | size_t RowOffset = 0; |
---|
| 1289 | for (int i = 0, ie = SourceRanks.size(); i != ie; ++i) { |
---|
| 1290 | readData(SourceRanks[i], RowOffset, Rank, TotalReadSize, NErrs); |
---|
| 1291 | RowOffset += readNumElems(SourceRanks[i]); |
---|
| 1292 | } |
---|
| 1293 | |
---|
| 1294 | DisableCollErrChecking = false; |
---|
| 1295 | } else { |
---|
| 1296 | readData(EffRank, 0, Rank, TotalReadSize, NErrs); |
---|
| 1297 | } |
---|
| 1298 | |
---|
| 1299 | int AllNErrs[3]; |
---|
| 1300 | #ifndef GENERICIO_NO_MPI |
---|
| 1301 | MPI_Allreduce(NErrs, AllNErrs, 3, MPI_INT, MPI_SUM, Comm); |
---|
| 1302 | #else |
---|
| 1303 | AllNErrs[0] = NErrs[0]; AllNErrs[1] = NErrs[1]; AllNErrs[2] = NErrs[2]; |
---|
| 1304 | #endif |
---|
| 1305 | |
---|
| 1306 | if (AllNErrs[0] > 0 || AllNErrs[1] > 0 || AllNErrs[2] > 0) { |
---|
| 1307 | stringstream ss; |
---|
| 1308 | ss << "Experienced " << AllNErrs[0] << " I/O error(s), " << |
---|
| 1309 | AllNErrs[1] << " CRC error(s) and " << AllNErrs[2] << |
---|
| 1310 | " decompression CRC error(s) reading: " << OpenFileName; |
---|
| 1311 | throw runtime_error(ss.str()); |
---|
| 1312 | } |
---|
| 1313 | |
---|
| 1314 | #ifndef GENERICIO_NO_MPI |
---|
| 1315 | MPI_Barrier(Comm); |
---|
| 1316 | #endif |
---|
| 1317 | |
---|
| 1318 | #ifndef GENERICIO_NO_MPI |
---|
| 1319 | double EndTime = MPI_Wtime(); |
---|
| 1320 | #else |
---|
| 1321 | double EndTime = double(clock())/CLOCKS_PER_SEC; |
---|
| 1322 | #endif |
---|
| 1323 | |
---|
| 1324 | double TotalTime = EndTime - StartTime; |
---|
| 1325 | double MaxTotalTime; |
---|
| 1326 | #ifndef GENERICIO_NO_MPI |
---|
| 1327 | if (CollStats) |
---|
| 1328 | MPI_Reduce(&TotalTime, &MaxTotalTime, 1, MPI_DOUBLE, MPI_MAX, 0, Comm); |
---|
| 1329 | else |
---|
| 1330 | #endif |
---|
| 1331 | MaxTotalTime = TotalTime; |
---|
| 1332 | |
---|
| 1333 | uint64_t AllTotalReadSize; |
---|
| 1334 | #ifndef GENERICIO_NO_MPI |
---|
| 1335 | if (CollStats) |
---|
| 1336 | MPI_Reduce(&TotalReadSize, &AllTotalReadSize, 1, MPI_UINT64_T, MPI_SUM, 0, Comm); |
---|
| 1337 | else |
---|
| 1338 | #endif |
---|
| 1339 | AllTotalReadSize = TotalReadSize; |
---|
| 1340 | |
---|
| 1341 | if (Rank == 0 && PrintStats) { |
---|
| 1342 | double Rate = ((double) AllTotalReadSize) / MaxTotalTime / (1024.*1024.); |
---|
[d6628a6] | 1343 | std::cout << "Read " << Vars.size() << " variables from " << FileName << |
---|
| 1344 | " (" << AllTotalReadSize << " bytes) in " << MaxTotalTime << "s: " << |
---|
| 1345 | Rate << " MB/s [excluding header read]" << std::endl; |
---|
[8f0a211] | 1346 | } |
---|
| 1347 | } |
---|
| 1348 | |
---|
| 1349 | void GenericIO::readData(int EffRank, size_t RowOffset, int Rank, |
---|
| 1350 | uint64_t &TotalReadSize, int NErrs[3]) { |
---|
| 1351 | if (FH.isBigEndian()) |
---|
| 1352 | readData<true>(EffRank, RowOffset, Rank, TotalReadSize, NErrs); |
---|
| 1353 | else |
---|
| 1354 | readData<false>(EffRank, RowOffset, Rank, TotalReadSize, NErrs); |
---|
| 1355 | } |
---|
| 1356 | |
---|
| 1357 | // Note: Errors from this function should be recoverable. This means that if |
---|
| 1358 | // one rank throws an exception, then all ranks should. |
---|
| 1359 | template <bool IsBigEndian> |
---|
| 1360 | void GenericIO::readData(int EffRank, size_t RowOffset, int Rank, |
---|
| 1361 | uint64_t &TotalReadSize, int NErrs[3]) { |
---|
| 1362 | openAndReadHeader(Redistributing ? MismatchRedistribute : MismatchAllowed, |
---|
| 1363 | EffRank, false); |
---|
[00587dc] | 1364 | |
---|
| 1365 | assert(FH.getHeaderCache().size() && "HeaderCache must not be empty"); |
---|
| 1366 | |
---|
| 1367 | if (EffRank == -1) |
---|
| 1368 | EffRank = Rank; |
---|
| 1369 | |
---|
[a4fee13] | 1370 | GlobalHeader<IsBigEndian> *GH = (GlobalHeader<IsBigEndian> *) &FH.getHeaderCache()[0]; |
---|
| 1371 | size_t RankIndex = getRankIndex<IsBigEndian>(EffRank, GH, RankMap, FH.getHeaderCache()); |
---|
[00587dc] | 1372 | |
---|
| 1373 | assert(RankIndex < GH->NRanks && "Invalid rank specified"); |
---|
| 1374 | |
---|
[a4fee13] | 1375 | RankHeader<IsBigEndian> *RH = (RankHeader<IsBigEndian> *) &FH.getHeaderCache()[GH->RanksStart + |
---|
[00587dc] | 1376 | RankIndex*GH->RanksSize]; |
---|
| 1377 | |
---|
| 1378 | for (size_t i = 0; i < Vars.size(); ++i) { |
---|
| 1379 | uint64_t Offset = RH->Start; |
---|
| 1380 | bool VarFound = false; |
---|
| 1381 | for (uint64_t j = 0; j < GH->NVars; ++j) { |
---|
[a4fee13] | 1382 | VariableHeader<IsBigEndian> *VH = (VariableHeader<IsBigEndian> *) &FH.getHeaderCache()[GH->VarsStart + |
---|
[00587dc] | 1383 | j*GH->VarsSize]; |
---|
| 1384 | |
---|
| 1385 | string VName(VH->Name, VH->Name + NameSize); |
---|
| 1386 | size_t VNameNull = VName.find('\0'); |
---|
| 1387 | if (VNameNull < NameSize) |
---|
| 1388 | VName.resize(VNameNull); |
---|
| 1389 | |
---|
| 1390 | uint64_t ReadSize = RH->NElems*VH->Size + CRCSize; |
---|
| 1391 | if (VName != Vars[i].Name) { |
---|
| 1392 | Offset += ReadSize; |
---|
| 1393 | continue; |
---|
| 1394 | } |
---|
| 1395 | |
---|
[5d57155] | 1396 | size_t ElementSize = VH->Size; |
---|
| 1397 | if (offsetof_safe(VH, ElementSize) < GH->VarsSize) |
---|
| 1398 | ElementSize = VH->ElementSize; |
---|
| 1399 | |
---|
[00587dc] | 1400 | VarFound = true; |
---|
| 1401 | bool IsFloat = (bool) (VH->Flags & FloatValue), |
---|
| 1402 | IsSigned = (bool) (VH->Flags & SignedValue); |
---|
| 1403 | if (VH->Size != Vars[i].Size) { |
---|
| 1404 | stringstream ss; |
---|
| 1405 | ss << "Size mismatch for variable " << Vars[i].Name << |
---|
| 1406 | " in: " << OpenFileName << ": current: " << Vars[i].Size << |
---|
| 1407 | ", file: " << VH->Size; |
---|
| 1408 | throw runtime_error(ss.str()); |
---|
[5d57155] | 1409 | } else if (ElementSize != Vars[i].ElementSize) { |
---|
| 1410 | stringstream ss; |
---|
| 1411 | ss << "Element size mismatch for variable " << Vars[i].Name << |
---|
| 1412 | " in: " << OpenFileName << ": current: " << Vars[i].ElementSize << |
---|
| 1413 | ", file: " << ElementSize; |
---|
| 1414 | throw runtime_error(ss.str()); |
---|
[00587dc] | 1415 | } else if (IsFloat != Vars[i].IsFloat) { |
---|
| 1416 | string Float("float"), Int("integer"); |
---|
| 1417 | stringstream ss; |
---|
| 1418 | ss << "Type mismatch for variable " << Vars[i].Name << |
---|
| 1419 | " in: " << OpenFileName << ": current: " << |
---|
| 1420 | (Vars[i].IsFloat ? Float : Int) << |
---|
| 1421 | ", file: " << (IsFloat ? Float : Int); |
---|
| 1422 | throw runtime_error(ss.str()); |
---|
| 1423 | } else if (IsSigned != Vars[i].IsSigned) { |
---|
| 1424 | string Signed("signed"), Uns("unsigned"); |
---|
| 1425 | stringstream ss; |
---|
| 1426 | ss << "Type mismatch for variable " << Vars[i].Name << |
---|
| 1427 | " in: " << OpenFileName << ": current: " << |
---|
| 1428 | (Vars[i].IsSigned ? Signed : Uns) << |
---|
| 1429 | ", file: " << (IsSigned ? Signed : Uns); |
---|
| 1430 | throw runtime_error(ss.str()); |
---|
| 1431 | } |
---|
| 1432 | |
---|
[8f0a211] | 1433 | size_t VarOffset = RowOffset*Vars[i].Size; |
---|
| 1434 | void *VarData = ((char *) Vars[i].Data) + VarOffset; |
---|
| 1435 | |
---|
[00587dc] | 1436 | vector<unsigned char> LData; |
---|
[8f0a211] | 1437 | void *Data = VarData; |
---|
[00587dc] | 1438 | bool HasExtraSpace = Vars[i].HasExtraSpace; |
---|
[a4fee13] | 1439 | if (offsetof_safe(GH, BlocksStart) < GH->GlobalHeaderSize && |
---|
[00587dc] | 1440 | GH->BlocksSize > 0) { |
---|
[a4fee13] | 1441 | BlockHeader<IsBigEndian> *BH = (BlockHeader<IsBigEndian> *) |
---|
[00587dc] | 1442 | &FH.getHeaderCache()[GH->BlocksStart + |
---|
| 1443 | (RankIndex*GH->NVars + j)*GH->BlocksSize]; |
---|
| 1444 | ReadSize = BH->Size + CRCSize; |
---|
| 1445 | Offset = BH->Start; |
---|
| 1446 | |
---|
| 1447 | if (strncmp(BH->Filters[0], CompressName, FilterNameSize) == 0) { |
---|
| 1448 | LData.resize(ReadSize); |
---|
| 1449 | Data = &LData[0]; |
---|
| 1450 | HasExtraSpace = true; |
---|
| 1451 | } else if (BH->Filters[0][0] != '\0') { |
---|
| 1452 | stringstream ss; |
---|
| 1453 | ss << "Unknown filter \"" << BH->Filters[0] << "\" on variable " << Vars[i].Name; |
---|
| 1454 | throw runtime_error(ss.str()); |
---|
| 1455 | } |
---|
| 1456 | } |
---|
| 1457 | |
---|
| 1458 | assert(HasExtraSpace && "Extra space required for reading"); |
---|
| 1459 | |
---|
| 1460 | char CRCSave[CRCSize]; |
---|
| 1461 | char *CRCLoc = ((char *) Data) + ReadSize - CRCSize; |
---|
| 1462 | if (HasExtraSpace) |
---|
| 1463 | std::copy(CRCLoc, CRCLoc + CRCSize, CRCSave); |
---|
| 1464 | |
---|
| 1465 | int Retry = 0; |
---|
| 1466 | { |
---|
| 1467 | int RetryCount = 300; |
---|
| 1468 | const char *EnvStr = getenv("GENERICIO_RETRY_COUNT"); |
---|
| 1469 | if (EnvStr) |
---|
| 1470 | RetryCount = atoi(EnvStr); |
---|
| 1471 | |
---|
| 1472 | int RetrySleep = 100; // ms |
---|
| 1473 | EnvStr = getenv("GENERICIO_RETRY_SLEEP"); |
---|
| 1474 | if (EnvStr) |
---|
| 1475 | RetrySleep = atoi(EnvStr); |
---|
| 1476 | |
---|
| 1477 | for (; Retry < RetryCount; ++Retry) { |
---|
| 1478 | try { |
---|
| 1479 | FH.get()->read(Data, ReadSize, Offset, Vars[i].Name); |
---|
| 1480 | break; |
---|
| 1481 | } catch (...) { } |
---|
| 1482 | |
---|
| 1483 | usleep(1000*RetrySleep); |
---|
| 1484 | } |
---|
| 1485 | |
---|
| 1486 | if (Retry == RetryCount) { |
---|
| 1487 | ++NErrs[0]; |
---|
| 1488 | break; |
---|
| 1489 | } else if (Retry > 0) { |
---|
| 1490 | EnvStr = getenv("GENERICIO_VERBOSE"); |
---|
| 1491 | if (EnvStr) { |
---|
| 1492 | int Mod = atoi(EnvStr); |
---|
| 1493 | if (Mod > 0) { |
---|
| 1494 | int Rank; |
---|
| 1495 | #ifndef GENERICIO_NO_MPI |
---|
| 1496 | MPI_Comm_rank(MPI_COMM_WORLD, &Rank); |
---|
| 1497 | #else |
---|
| 1498 | Rank = 0; |
---|
| 1499 | #endif |
---|
| 1500 | |
---|
| 1501 | std::cerr << "Rank " << Rank << ": " << Retry << |
---|
| 1502 | " I/O retries were necessary for reading " << |
---|
| 1503 | Vars[i].Name << " from: " << OpenFileName << "\n"; |
---|
| 1504 | |
---|
| 1505 | std::cerr.flush(); |
---|
| 1506 | } |
---|
| 1507 | } |
---|
| 1508 | } |
---|
| 1509 | } |
---|
| 1510 | |
---|
| 1511 | TotalReadSize += ReadSize; |
---|
| 1512 | |
---|
| 1513 | uint64_t CRC = crc64_omp(Data, ReadSize); |
---|
| 1514 | if (CRC != (uint64_t) -1) { |
---|
| 1515 | ++NErrs[1]; |
---|
| 1516 | |
---|
| 1517 | int Rank; |
---|
| 1518 | #ifndef GENERICIO_NO_MPI |
---|
| 1519 | MPI_Comm_rank(MPI_COMM_WORLD, &Rank); |
---|
| 1520 | #else |
---|
| 1521 | Rank = 0; |
---|
| 1522 | #endif |
---|
| 1523 | |
---|
| 1524 | // All ranks will do this and have a good time! |
---|
| 1525 | string dn = "gio_crc_errors"; |
---|
| 1526 | mkdir(dn.c_str(), 0777); |
---|
| 1527 | |
---|
| 1528 | srand(time(0)); |
---|
| 1529 | int DumpNum = rand(); |
---|
| 1530 | stringstream ssd; |
---|
| 1531 | ssd << dn << "/gio_crc_error_dump." << Rank << "." << DumpNum << ".bin"; |
---|
| 1532 | |
---|
| 1533 | stringstream ss; |
---|
| 1534 | ss << dn << "/gio_crc_error_log." << Rank << ".txt"; |
---|
| 1535 | |
---|
| 1536 | ofstream ofs(ss.str().c_str(), ofstream::out | ofstream::app); |
---|
| 1537 | ofs << "On-Disk CRC Error Report:\n"; |
---|
| 1538 | ofs << "Variable: " << Vars[i].Name << "\n"; |
---|
| 1539 | ofs << "File: " << OpenFileName << "\n"; |
---|
| 1540 | ofs << "I/O Retries: " << Retry << "\n"; |
---|
| 1541 | ofs << "Size: " << ReadSize << " bytes\n"; |
---|
| 1542 | ofs << "Offset: " << Offset << " bytes\n"; |
---|
| 1543 | ofs << "CRC: " << CRC << " (expected is -1)\n"; |
---|
| 1544 | ofs << "Dump file: " << ssd.str() << "\n"; |
---|
| 1545 | ofs << "\n"; |
---|
| 1546 | ofs.close(); |
---|
| 1547 | |
---|
| 1548 | ofstream dofs(ssd.str().c_str(), ofstream::out); |
---|
| 1549 | dofs.write((const char *) Data, ReadSize); |
---|
| 1550 | dofs.close(); |
---|
[14e73bb] | 1551 | |
---|
| 1552 | uint64_t RawCRC = crc64_omp(Data, ReadSize - CRCSize); |
---|
| 1553 | unsigned char *UData = (unsigned char *) Data; |
---|
| 1554 | crc64_invert(RawCRC, &UData[ReadSize - CRCSize]); |
---|
| 1555 | uint64_t NewCRC = crc64_omp(Data, ReadSize); |
---|
| 1556 | std::cerr << "Recalulated CRC: " << NewCRC << ((NewCRC == -1) ? "ok" : "bad") << "\n"; |
---|
[00587dc] | 1557 | break; |
---|
| 1558 | } |
---|
| 1559 | |
---|
| 1560 | if (HasExtraSpace) |
---|
| 1561 | std::copy(CRCSave, CRCSave + CRCSize, CRCLoc); |
---|
| 1562 | |
---|
| 1563 | if (LData.size()) { |
---|
[a4fee13] | 1564 | CompressHeader<IsBigEndian> *CH = (CompressHeader<IsBigEndian>*) &LData[0]; |
---|
[00587dc] | 1565 | |
---|
| 1566 | #ifdef _OPENMP |
---|
| 1567 | #pragma omp master |
---|
| 1568 | { |
---|
| 1569 | #endif |
---|
| 1570 | |
---|
| 1571 | if (!blosc_initialized) { |
---|
| 1572 | blosc_init(); |
---|
| 1573 | blosc_initialized = true; |
---|
| 1574 | } |
---|
| 1575 | |
---|
| 1576 | #ifdef _OPENMP |
---|
| 1577 | blosc_set_nthreads(omp_get_max_threads()); |
---|
| 1578 | } |
---|
| 1579 | #endif |
---|
| 1580 | |
---|
[a4fee13] | 1581 | blosc_decompress(&LData[0] + sizeof(CompressHeader<IsBigEndian>), |
---|
[8f0a211] | 1582 | VarData, Vars[i].Size*RH->NElems); |
---|
[00587dc] | 1583 | |
---|
[8f0a211] | 1584 | if (CH->OrigCRC != crc64_omp(VarData, Vars[i].Size*RH->NElems)) { |
---|
[00587dc] | 1585 | ++NErrs[2]; |
---|
| 1586 | break; |
---|
| 1587 | } |
---|
| 1588 | } |
---|
| 1589 | |
---|
[a4fee13] | 1590 | // Byte swap the data if necessary. |
---|
| 1591 | if (IsBigEndian != isBigEndian()) |
---|
[5d57155] | 1592 | for (size_t j = 0; |
---|
| 1593 | j < RH->NElems*(Vars[i].Size/Vars[i].ElementSize); ++j) { |
---|
| 1594 | char *Offset = ((char *) VarData) + j*Vars[i].ElementSize; |
---|
| 1595 | bswap(Offset, Vars[i].ElementSize); |
---|
[a4fee13] | 1596 | } |
---|
| 1597 | |
---|
[00587dc] | 1598 | break; |
---|
| 1599 | } |
---|
| 1600 | |
---|
| 1601 | if (!VarFound) |
---|
| 1602 | throw runtime_error("Variable " + Vars[i].Name + |
---|
| 1603 | " not found in: " + OpenFileName); |
---|
| 1604 | |
---|
| 1605 | // This is for debugging. |
---|
| 1606 | if (NErrs[0] || NErrs[1] || NErrs[2]) { |
---|
| 1607 | const char *EnvStr = getenv("GENERICIO_VERBOSE"); |
---|
| 1608 | if (EnvStr) { |
---|
| 1609 | int Mod = atoi(EnvStr); |
---|
| 1610 | if (Mod > 0) { |
---|
| 1611 | int Rank; |
---|
| 1612 | #ifndef GENERICIO_NO_MPI |
---|
| 1613 | MPI_Comm_rank(MPI_COMM_WORLD, &Rank); |
---|
| 1614 | #else |
---|
| 1615 | Rank = 0; |
---|
| 1616 | #endif |
---|
| 1617 | |
---|
| 1618 | std::cerr << "Rank " << Rank << ": " << NErrs[0] << " I/O error(s), " << |
---|
| 1619 | NErrs[1] << " CRC error(s) and " << NErrs[2] << |
---|
| 1620 | " decompression CRC error(s) reading: " << Vars[i].Name << |
---|
| 1621 | " from: " << OpenFileName << "\n"; |
---|
| 1622 | |
---|
| 1623 | std::cerr.flush(); |
---|
| 1624 | } |
---|
| 1625 | } |
---|
| 1626 | } |
---|
| 1627 | |
---|
| 1628 | if (NErrs[0] || NErrs[1] || NErrs[2]) |
---|
| 1629 | break; |
---|
| 1630 | } |
---|
| 1631 | } |
---|
| 1632 | |
---|
| 1633 | void GenericIO::getVariableInfo(vector<VariableInfo> &VI) { |
---|
[a4fee13] | 1634 | if (FH.isBigEndian()) |
---|
| 1635 | getVariableInfo<true>(VI); |
---|
| 1636 | else |
---|
| 1637 | getVariableInfo<false>(VI); |
---|
| 1638 | } |
---|
| 1639 | |
---|
| 1640 | template <bool IsBigEndian> |
---|
| 1641 | void GenericIO::getVariableInfo(vector<VariableInfo> &VI) { |
---|
[00587dc] | 1642 | assert(FH.getHeaderCache().size() && "HeaderCache must not be empty"); |
---|
| 1643 | |
---|
[a4fee13] | 1644 | GlobalHeader<IsBigEndian> *GH = (GlobalHeader<IsBigEndian> *) &FH.getHeaderCache()[0]; |
---|
[00587dc] | 1645 | for (uint64_t j = 0; j < GH->NVars; ++j) { |
---|
[a4fee13] | 1646 | VariableHeader<IsBigEndian> *VH = (VariableHeader<IsBigEndian> *) &FH.getHeaderCache()[GH->VarsStart + |
---|
[00587dc] | 1647 | j*GH->VarsSize]; |
---|
| 1648 | |
---|
| 1649 | string VName(VH->Name, VH->Name + NameSize); |
---|
| 1650 | size_t VNameNull = VName.find('\0'); |
---|
| 1651 | if (VNameNull < NameSize) |
---|
| 1652 | VName.resize(VNameNull); |
---|
| 1653 | |
---|
[5d57155] | 1654 | size_t ElementSize = VH->Size; |
---|
| 1655 | if (offsetof_safe(VH, ElementSize) < GH->VarsSize) |
---|
| 1656 | ElementSize = VH->ElementSize; |
---|
| 1657 | |
---|
[00587dc] | 1658 | bool IsFloat = (bool) (VH->Flags & FloatValue), |
---|
| 1659 | IsSigned = (bool) (VH->Flags & SignedValue), |
---|
| 1660 | IsPhysCoordX = (bool) (VH->Flags & ValueIsPhysCoordX), |
---|
| 1661 | IsPhysCoordY = (bool) (VH->Flags & ValueIsPhysCoordY), |
---|
| 1662 | IsPhysCoordZ = (bool) (VH->Flags & ValueIsPhysCoordZ), |
---|
| 1663 | MaybePhysGhost = (bool) (VH->Flags & ValueMaybePhysGhost); |
---|
| 1664 | VI.push_back(VariableInfo(VName, (size_t) VH->Size, IsFloat, IsSigned, |
---|
| 1665 | IsPhysCoordX, IsPhysCoordY, IsPhysCoordZ, |
---|
[5d57155] | 1666 | MaybePhysGhost, ElementSize)); |
---|
[00587dc] | 1667 | } |
---|
| 1668 | } |
---|
| 1669 | |
---|
| 1670 | void GenericIO::setNaturalDefaultPartition() { |
---|
| 1671 | #ifdef __bgq__ |
---|
[14e73bb] | 1672 | DefaultPartition = MPIX_IO_link_id(); |
---|
[00587dc] | 1673 | #else |
---|
| 1674 | #ifndef GENERICIO_NO_MPI |
---|
| 1675 | bool UseName = true; |
---|
| 1676 | const char *EnvStr = getenv("GENERICIO_PARTITIONS_USE_NAME"); |
---|
| 1677 | if (EnvStr) { |
---|
| 1678 | int Mod = atoi(EnvStr); |
---|
| 1679 | UseName = (Mod != 0); |
---|
| 1680 | } |
---|
| 1681 | |
---|
| 1682 | if (UseName) { |
---|
| 1683 | // This is a heuristic to generate ~256 partitions based on the |
---|
| 1684 | // names of the nodes. |
---|
| 1685 | char Name[MPI_MAX_PROCESSOR_NAME]; |
---|
| 1686 | int Len = 0; |
---|
| 1687 | |
---|
| 1688 | MPI_Get_processor_name(Name, &Len); |
---|
| 1689 | unsigned char color = 0; |
---|
| 1690 | for (int i = 0; i < Len; ++i) |
---|
| 1691 | color += (unsigned char) Name[i]; |
---|
| 1692 | |
---|
| 1693 | DefaultPartition = color; |
---|
| 1694 | } |
---|
| 1695 | |
---|
| 1696 | // This is for debugging. |
---|
| 1697 | EnvStr = getenv("GENERICIO_RANK_PARTITIONS"); |
---|
| 1698 | if (EnvStr) { |
---|
| 1699 | int Mod = atoi(EnvStr); |
---|
| 1700 | if (Mod > 0) { |
---|
| 1701 | int Rank; |
---|
| 1702 | MPI_Comm_rank(MPI_COMM_WORLD, &Rank); |
---|
| 1703 | DefaultPartition += Rank % Mod; |
---|
| 1704 | } |
---|
| 1705 | } |
---|
| 1706 | #endif |
---|
| 1707 | #endif |
---|
| 1708 | } |
---|
| 1709 | |
---|
| 1710 | } /* END namespace cosmotk */ |
---|