[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 | #ifndef GENERICIO_H |
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| 43 | #define GENERICIO_H |
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| 44 | |
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| 45 | #include <cstdlib> |
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| 46 | #include <vector> |
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| 47 | #include <string> |
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| 48 | #include <iostream> |
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| 49 | #include <limits> |
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| 50 | #include <stdint.h> |
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| 51 | |
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| 52 | #ifndef GENERICIO_NO_MPI |
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| 53 | #include <mpi.h> |
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| 54 | #else |
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| 55 | #include <fstream> |
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| 56 | #endif |
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| 57 | |
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| 58 | #include <unistd.h> |
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| 59 | |
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| 60 | namespace gio { |
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| 61 | |
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| 62 | class GenericFileIO { |
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| 63 | public: |
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| 64 | virtual ~GenericFileIO() {} |
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| 65 | |
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| 66 | public: |
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| 67 | virtual void open(const std::string &FN, bool ForReading = false) = 0; |
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| 68 | virtual void setSize(size_t sz) = 0; |
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| 69 | virtual void read(void *buf, size_t count, off_t offset, |
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| 70 | const std::string &D) = 0; |
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| 71 | virtual void write(const void *buf, size_t count, off_t offset, |
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| 72 | const std::string &D) = 0; |
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| 73 | |
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| 74 | protected: |
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| 75 | std::string FileName; |
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| 76 | }; |
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| 77 | |
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| 78 | #ifndef GENERICIO_NO_MPI |
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| 79 | class GenericFileIO_MPI : public GenericFileIO { |
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| 80 | public: |
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| 81 | GenericFileIO_MPI(const MPI_Comm &C) : FH(MPI_FILE_NULL), Comm(C) {} |
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| 82 | virtual ~GenericFileIO_MPI(); |
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| 83 | |
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| 84 | public: |
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| 85 | virtual void open(const std::string &FN, bool ForReading = false); |
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| 86 | virtual void setSize(size_t sz); |
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| 87 | virtual void read(void *buf, size_t count, off_t offset, const std::string &D); |
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| 88 | virtual void write(const void *buf, size_t count, off_t offset, const std::string &D); |
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| 89 | |
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| 90 | protected: |
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| 91 | MPI_File FH; |
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| 92 | MPI_Comm Comm; |
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| 93 | }; |
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| 94 | |
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| 95 | class GenericFileIO_MPICollective : public GenericFileIO_MPI { |
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| 96 | public: |
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| 97 | GenericFileIO_MPICollective(const MPI_Comm &C) : GenericFileIO_MPI(C) {} |
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| 98 | |
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| 99 | public: |
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| 100 | void read(void *buf, size_t count, off_t offset, const std::string &D); |
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| 101 | void write(const void *buf, size_t count, off_t offset, const std::string &D); |
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| 102 | }; |
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| 103 | #endif |
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| 104 | |
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| 105 | class GenericFileIO_POSIX : public GenericFileIO { |
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| 106 | public: |
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| 107 | GenericFileIO_POSIX() : FH(-1) {} |
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| 108 | ~GenericFileIO_POSIX(); |
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| 109 | |
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| 110 | public: |
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| 111 | void open(const std::string &FN, bool ForReading = false); |
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| 112 | void setSize(size_t sz); |
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| 113 | void read(void *buf, size_t count, off_t offset, const std::string &D); |
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| 114 | void write(const void *buf, size_t count, off_t offset, const std::string &D); |
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| 115 | |
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| 116 | protected: |
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| 117 | int FH; |
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| 118 | }; |
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| 119 | |
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| 120 | class GenericIO { |
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| 121 | public: |
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| 122 | enum VariableFlags { |
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| 123 | VarHasExtraSpace = (1 << 0), // Note that this flag indicates that the |
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| 124 | // extra space is available, but the GenericIO |
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| 125 | // implementation is required to |
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| 126 | // preserve its contents. |
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| 127 | VarIsPhysCoordX = (1 << 1), |
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| 128 | VarIsPhysCoordY = (1 << 2), |
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| 129 | VarIsPhysCoordZ = (1 << 3), |
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| 130 | VarMaybePhysGhost = (1 << 4) |
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| 131 | }; |
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| 132 | |
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| 133 | struct VariableInfo { |
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| 134 | VariableInfo(const std::string &N, std::size_t S, bool IF, bool IS, |
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| 135 | bool PCX, bool PCY, bool PCZ, bool PG) |
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| 136 | : Name(N), Size(S), IsFloat(IF), IsSigned(IS), |
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| 137 | IsPhysCoordX(PCX), IsPhysCoordY(PCY), IsPhysCoordZ(PCZ), |
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| 138 | MaybePhysGhost(PG) {} |
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| 139 | |
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| 140 | std::string Name; |
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| 141 | std::size_t Size; |
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| 142 | bool IsFloat; |
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| 143 | bool IsSigned; |
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| 144 | bool IsPhysCoordX, IsPhysCoordY, IsPhysCoordZ; |
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| 145 | bool MaybePhysGhost; |
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| 146 | }; |
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| 147 | |
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| 148 | public: |
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| 149 | struct Variable { |
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| 150 | template <typename T> |
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| 151 | Variable(const std::string &N, T* D, unsigned Flags = 0) |
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| 152 | : Name(N), Size(sizeof(T)), |
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| 153 | IsFloat(!std::numeric_limits<T>::is_integer), |
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| 154 | IsSigned(std::numeric_limits<T>::is_signed), |
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| 155 | Data((void *) D), HasExtraSpace(Flags & VarHasExtraSpace), |
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| 156 | IsPhysCoordX(Flags & VarIsPhysCoordX), |
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| 157 | IsPhysCoordY(Flags & VarIsPhysCoordY), |
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| 158 | IsPhysCoordZ(Flags & VarIsPhysCoordZ), |
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| 159 | MaybePhysGhost(Flags & VarMaybePhysGhost) {} |
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| 160 | |
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| 161 | Variable(const VariableInfo &VI, void *D, unsigned Flags = 0) |
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| 162 | : Name(VI.Name), Size(VI.Size), IsFloat(VI.IsFloat), |
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| 163 | IsSigned(VI.IsSigned), Data(D), |
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| 164 | HasExtraSpace(Flags & VarHasExtraSpace), |
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| 165 | IsPhysCoordX((Flags & VarIsPhysCoordX) || VI.IsPhysCoordX), |
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| 166 | IsPhysCoordY((Flags & VarIsPhysCoordY) || VI.IsPhysCoordY), |
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| 167 | IsPhysCoordZ((Flags & VarIsPhysCoordZ) || VI.IsPhysCoordZ), |
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| 168 | MaybePhysGhost((Flags & VarMaybePhysGhost) || VI.MaybePhysGhost) {} |
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| 169 | |
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| 170 | std::string Name; |
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| 171 | std::size_t Size; |
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| 172 | bool IsFloat; |
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| 173 | bool IsSigned; |
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| 174 | void *Data; |
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| 175 | bool HasExtraSpace; |
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| 176 | bool IsPhysCoordX, IsPhysCoordY, IsPhysCoordZ; |
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| 177 | bool MaybePhysGhost; |
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| 178 | }; |
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| 179 | |
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| 180 | public: |
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| 181 | enum FileIO { |
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| 182 | FileIOMPI, |
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| 183 | FileIOPOSIX, |
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| 184 | FileIOMPICollective |
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| 185 | }; |
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| 186 | |
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| 187 | #ifndef GENERICIO_NO_MPI |
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| 188 | GenericIO(const MPI_Comm &C, const std::string &FN, unsigned FIOT = -1) |
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| 189 | : NElems(0), FileIOType(FIOT == (unsigned) -1 ? DefaultFileIOType : FIOT), |
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[8f0a211] | 190 | Partition(DefaultPartition), Comm(C), FileName(FN), Redistributing(false), |
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| 191 | DisableCollErrChecking(false), SplitComm(MPI_COMM_NULL) { |
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[00587dc] | 192 | std::fill(PhysOrigin, PhysOrigin + 3, 0.0); |
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| 193 | std::fill(PhysScale, PhysScale + 3, 0.0); |
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| 194 | } |
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| 195 | #else |
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| 196 | GenericIO(const std::string &FN, unsigned FIOT = -1) |
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| 197 | : NElems(0), FileIOType(FIOT == (unsigned) -1 ? DefaultFileIOType : FIOT), |
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[8f0a211] | 198 | Partition(DefaultPartition), FileName(FN), Redistributing(false), |
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| 199 | DisableCollErrChecking(false) { |
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[00587dc] | 200 | std::fill(PhysOrigin, PhysOrigin + 3, 0.0); |
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| 201 | std::fill(PhysScale, PhysScale + 3, 0.0); |
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| 202 | } |
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| 203 | #endif |
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| 204 | |
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| 205 | ~GenericIO() { |
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| 206 | close(); |
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| 207 | |
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| 208 | #ifndef GENERICIO_NO_MPI |
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| 209 | if (SplitComm != MPI_COMM_NULL) |
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| 210 | MPI_Comm_free(&SplitComm); |
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| 211 | #endif |
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| 212 | } |
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| 213 | |
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| 214 | public: |
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| 215 | std::size_t requestedExtraSpace() const { |
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| 216 | return 8; |
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| 217 | } |
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| 218 | |
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| 219 | void setNumElems(std::size_t E) { |
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| 220 | NElems = E; |
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| 221 | |
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| 222 | #ifndef GENERICIO_NO_MPI |
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| 223 | int IsLarge = E >= CollectiveMPIIOThreshold; |
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| 224 | int AllIsLarge; |
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| 225 | MPI_Allreduce(&IsLarge, &AllIsLarge, 1, MPI_INT, MPI_SUM, Comm); |
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| 226 | if (!AllIsLarge) |
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| 227 | FileIOType = FileIOMPICollective; |
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| 228 | #endif |
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| 229 | } |
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| 230 | |
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| 231 | void setPhysOrigin(double O, int Dim = -1) { |
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| 232 | if (Dim >= 0) |
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| 233 | PhysOrigin[Dim] = O; |
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| 234 | else |
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| 235 | std::fill(PhysOrigin, PhysOrigin + 3, O); |
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| 236 | } |
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| 237 | |
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| 238 | void setPhysScale(double S, int Dim = -1) { |
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| 239 | if (Dim >= 0) |
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| 240 | PhysScale[Dim] = S; |
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| 241 | else |
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| 242 | std::fill(PhysScale, PhysScale + 3, S); |
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| 243 | } |
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| 244 | |
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| 245 | template <typename T> |
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| 246 | void addVariable(const std::string &Name, T *Data, |
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| 247 | unsigned Flags = 0) { |
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| 248 | Vars.push_back(Variable(Name, Data, Flags)); |
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| 249 | } |
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| 250 | |
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| 251 | template <typename T, typename A> |
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| 252 | void addVariable(const std::string &Name, std::vector<T, A> &Data, |
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| 253 | unsigned Flags = 0) { |
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| 254 | T *D = Data.empty() ? 0 : &Data[0]; |
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| 255 | addVariable(Name, D, Flags); |
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| 256 | } |
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| 257 | |
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| 258 | void addVariable(const VariableInfo &VI, void *Data, |
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| 259 | unsigned Flags = 0) { |
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| 260 | Vars.push_back(Variable(VI, Data, Flags)); |
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| 261 | } |
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| 262 | |
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| 263 | #ifndef GENERICIO_NO_MPI |
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| 264 | // Writing |
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| 265 | void write(); |
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| 266 | #endif |
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| 267 | |
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[8f0a211] | 268 | enum MismatchBehavior { |
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| 269 | MismatchAllowed, |
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| 270 | MismatchDisallowed, |
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| 271 | MismatchRedistribute |
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| 272 | }; |
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| 273 | |
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[00587dc] | 274 | // Reading |
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[8f0a211] | 275 | void openAndReadHeader(MismatchBehavior MB = MismatchDisallowed, |
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| 276 | int EffRank = -1, bool CheckPartMap = true); |
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[00587dc] | 277 | |
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| 278 | int readNRanks(); |
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| 279 | void readDims(int Dims[3]); |
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| 280 | |
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| 281 | // Note: For partitioned inputs, this returns -1. |
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| 282 | uint64_t readTotalNumElems(); |
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| 283 | |
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| 284 | void readPhysOrigin(double Origin[3]); |
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| 285 | void readPhysScale(double Scale[3]); |
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| 286 | |
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| 287 | void clearVariables() { this->Vars.clear(); }; |
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| 288 | |
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| 289 | int getNumberOfVariables() { return this->Vars.size(); }; |
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| 290 | |
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| 291 | void getVariableInfo(std::vector<VariableInfo> &VI); |
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| 292 | |
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| 293 | std::size_t readNumElems(int EffRank = -1); |
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| 294 | void readCoords(int Coords[3], int EffRank = -1); |
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| 295 | int readGlobalRankNumber(int EffRank = -1); |
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| 296 | |
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[a4fee13] | 297 | void readData(int EffRank = -1, bool PrintStats = true, bool CollStats = true); |
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[00587dc] | 298 | |
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| 299 | void close() { |
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| 300 | FH.close(); |
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| 301 | } |
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| 302 | |
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| 303 | void setPartition(int P) { |
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| 304 | Partition = P; |
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| 305 | } |
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| 306 | |
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| 307 | static void setDefaultFileIOType(unsigned FIOT) { |
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| 308 | DefaultFileIOType = FIOT; |
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| 309 | } |
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| 310 | |
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| 311 | static void setDefaultPartition(int P) { |
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| 312 | DefaultPartition = P; |
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| 313 | } |
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| 314 | |
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| 315 | static void setNaturalDefaultPartition(); |
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| 316 | |
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| 317 | static void setDefaultShouldCompress(bool C) { |
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| 318 | DefaultShouldCompress = C; |
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| 319 | } |
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| 320 | |
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| 321 | #ifndef GENERICIO_NO_MPI |
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| 322 | static void setCollectiveMPIIOThreshold(std::size_t T) { |
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| 323 | #ifndef GENERICIO_NO_NEVER_USE_COLLECTIVE_IO |
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| 324 | CollectiveMPIIOThreshold = T; |
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| 325 | #endif |
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| 326 | } |
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| 327 | #endif |
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| 328 | |
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[a4fee13] | 329 | private: |
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| 330 | // Implementation functions templated on the Endianness of the underlying |
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| 331 | // data. |
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| 332 | |
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| 333 | #ifndef GENERICIO_NO_MPI |
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| 334 | template <bool IsBigEndian> |
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| 335 | void write(); |
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| 336 | #endif |
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| 337 | |
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| 338 | template <bool IsBigEndian> |
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[8f0a211] | 339 | void readHeaderLeader(void *GHPtr, MismatchBehavior MB, int Rank, int NRanks, |
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| 340 | int SplitNRanks, std::string &LocalFileName, |
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| 341 | uint64_t &HeaderSize, std::vector<char> &Header); |
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[a4fee13] | 342 | |
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| 343 | template <bool IsBigEndian> |
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| 344 | int readNRanks(); |
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| 345 | |
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| 346 | template <bool IsBigEndian> |
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| 347 | void readDims(int Dims[3]); |
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| 348 | |
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| 349 | template <bool IsBigEndian> |
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| 350 | uint64_t readTotalNumElems(); |
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| 351 | |
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| 352 | template <bool IsBigEndian> |
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| 353 | void readPhysOrigin(double Origin[3]); |
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| 354 | |
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| 355 | template <bool IsBigEndian> |
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| 356 | void readPhysScale(double Scale[3]); |
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| 357 | |
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| 358 | template <bool IsBigEndian> |
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| 359 | int readGlobalRankNumber(int EffRank); |
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| 360 | |
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| 361 | template <bool IsBigEndian> |
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| 362 | size_t readNumElems(int EffRank); |
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| 363 | |
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| 364 | template <bool IsBigEndian> |
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| 365 | void readCoords(int Coords[3], int EffRank); |
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| 366 | |
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[8f0a211] | 367 | void readData(int EffRank, size_t RowOffset, int Rank, |
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| 368 | uint64_t &TotalReadSize, int NErrs[3]); |
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| 369 | |
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[a4fee13] | 370 | template <bool IsBigEndian> |
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[8f0a211] | 371 | void readData(int EffRank, size_t RowOffset, |
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| 372 | int Rank, uint64_t &TotalReadSize, int NErrs[3]); |
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[a4fee13] | 373 | |
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| 374 | template <bool IsBigEndian> |
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| 375 | void getVariableInfo(std::vector<VariableInfo> &VI); |
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| 376 | |
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[00587dc] | 377 | protected: |
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| 378 | std::vector<Variable> Vars; |
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| 379 | std::size_t NElems; |
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| 380 | |
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| 381 | double PhysOrigin[3], PhysScale[3]; |
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| 382 | |
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| 383 | unsigned FileIOType; |
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| 384 | int Partition; |
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| 385 | #ifndef GENERICIO_NO_MPI |
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| 386 | MPI_Comm Comm; |
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| 387 | #endif |
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| 388 | std::string FileName; |
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| 389 | |
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| 390 | static unsigned DefaultFileIOType; |
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| 391 | static int DefaultPartition; |
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| 392 | static bool DefaultShouldCompress; |
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| 393 | |
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| 394 | #ifndef GENERICIO_NO_MPI |
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| 395 | static std::size_t CollectiveMPIIOThreshold; |
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| 396 | #endif |
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| 397 | |
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[8f0a211] | 398 | // When redistributing, the rank blocks which this process should read. |
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| 399 | bool Redistributing, DisableCollErrChecking; |
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| 400 | std::vector<int> SourceRanks; |
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| 401 | |
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[00587dc] | 402 | std::vector<int> RankMap; |
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| 403 | #ifndef GENERICIO_NO_MPI |
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| 404 | MPI_Comm SplitComm; |
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| 405 | #endif |
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| 406 | std::string OpenFileName; |
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| 407 | |
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| 408 | // This reference counting mechanism allows the the GenericIO class |
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| 409 | // to be used in a cursor mode. To do this, make a copy of the class |
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| 410 | // after reading the header but prior to adding the variables. |
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| 411 | struct FHManager { |
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| 412 | FHManager() : CountedFH(0) { |
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| 413 | allocate(); |
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| 414 | } |
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| 415 | |
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| 416 | FHManager(const FHManager& F) { |
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| 417 | CountedFH = F.CountedFH; |
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| 418 | CountedFH->Cnt += 1; |
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| 419 | } |
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| 420 | |
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| 421 | ~FHManager() { |
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| 422 | close(); |
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| 423 | } |
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| 424 | |
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| 425 | GenericFileIO *&get() { |
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| 426 | if (!CountedFH) |
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| 427 | allocate(); |
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| 428 | |
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| 429 | return CountedFH->GFIO; |
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| 430 | } |
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| 431 | |
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| 432 | std::vector<char> &getHeaderCache() { |
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| 433 | if (!CountedFH) |
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| 434 | allocate(); |
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| 435 | |
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| 436 | return CountedFH->HeaderCache; |
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| 437 | } |
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| 438 | |
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[a4fee13] | 439 | bool isBigEndian() { |
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| 440 | return CountedFH ? CountedFH->IsBigEndian : false; |
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| 441 | } |
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| 442 | |
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| 443 | void setIsBigEndian(bool isBE) { |
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| 444 | CountedFH->IsBigEndian = isBE; |
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| 445 | } |
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| 446 | |
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[00587dc] | 447 | void allocate() { |
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| 448 | close(); |
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| 449 | CountedFH = new FHWCnt; |
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| 450 | }; |
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| 451 | |
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| 452 | void close() { |
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| 453 | if (CountedFH && CountedFH->Cnt == 1) |
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| 454 | delete CountedFH; |
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| 455 | else if (CountedFH) |
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| 456 | CountedFH->Cnt -= 1; |
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| 457 | |
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| 458 | CountedFH = 0; |
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| 459 | } |
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| 460 | |
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| 461 | struct FHWCnt { |
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[a4fee13] | 462 | FHWCnt() : GFIO(0), Cnt(1), IsBigEndian(false) {} |
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[00587dc] | 463 | |
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| 464 | ~FHWCnt() { |
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| 465 | close(); |
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| 466 | } |
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| 467 | |
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| 468 | protected: |
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| 469 | void close() { |
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| 470 | delete GFIO; |
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| 471 | GFIO = 0; |
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| 472 | } |
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| 473 | |
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| 474 | public: |
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| 475 | GenericFileIO *GFIO; |
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| 476 | size_t Cnt; |
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| 477 | |
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| 478 | // Used for reading |
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| 479 | std::vector<char> HeaderCache; |
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[a4fee13] | 480 | bool IsBigEndian; |
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[00587dc] | 481 | }; |
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| 482 | |
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| 483 | FHWCnt *CountedFH; |
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| 484 | } FH; |
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| 485 | }; |
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| 486 | |
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| 487 | } /* END namespace cosmotk */ |
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| 488 | #endif // GENERICIO_H |
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| 489 | |
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