1 | #include <fstream> |
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2 | |
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3 | #include "onetcdf4.hpp" |
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4 | #include "group_template.hpp" |
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5 | #include "mpi.hpp" |
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6 | #include "netcdf.hpp" |
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7 | #include "netCdfInterface.hpp" |
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8 | #include "netCdfException.hpp" |
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9 | |
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10 | namespace xios |
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11 | { |
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12 | /// ////////////////////// Définitions ////////////////////// /// |
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13 | |
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14 | CONetCDF4::CONetCDF4 |
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15 | (const StdString & filename, bool append, bool useClassicFormat, const MPI_Comm* comm, bool multifile) |
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16 | : path() |
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17 | , wmpi(false) |
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18 | , useClassicFormat(useClassicFormat) |
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19 | , recordOffset(0) |
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20 | { |
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21 | this->initialize(filename, append, useClassicFormat, comm,multifile); |
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22 | } |
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23 | |
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24 | //--------------------------------------------------------------- |
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25 | |
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26 | |
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27 | CONetCDF4::~CONetCDF4(void) |
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28 | { |
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29 | // CheckError(nc_close(this->ncidp)); |
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30 | } |
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31 | |
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32 | ///-------------------------------------------------------------- |
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33 | |
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34 | void CONetCDF4::initialize |
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35 | (const StdString & filename, bool append, bool useClassicFormat, const MPI_Comm* comm, bool multifile) |
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36 | { |
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37 | this->useClassicFormat = useClassicFormat; |
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38 | |
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39 | int mode = useClassicFormat ? 0 : NC_NETCDF4; |
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40 | |
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41 | // Don't use parallel mode if there is only one process |
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42 | if (comm) |
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43 | { |
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44 | int commSize = 0; |
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45 | MPI_Comm_size(*comm, &commSize); |
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46 | if (commSize <= 1) |
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47 | comm = NULL; |
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48 | } |
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49 | wmpi = comm && !multifile; |
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50 | |
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51 | if (wmpi) |
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52 | mode |= useClassicFormat ? NC_PNETCDF : NC_MPIIO; |
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53 | |
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54 | // If the file does not exist, we always create it |
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55 | if (!append || !std::ifstream(filename.c_str())) |
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56 | { |
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57 | if (wmpi) |
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58 | CNetCdfInterface::createPar(filename, mode, *comm, MPI_INFO_NULL, this->ncidp); |
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59 | else |
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60 | CNetCdfInterface::create(filename, mode, this->ncidp); |
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61 | |
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62 | this->appendMode = false; |
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63 | this->recordOffset = 0; |
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64 | } |
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65 | else |
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66 | { |
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67 | mode |= NC_WRITE; |
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68 | if (wmpi) |
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69 | CNetCdfInterface::openPar(filename, mode, *comm, MPI_INFO_NULL, this->ncidp); |
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70 | else |
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71 | CNetCdfInterface::open(filename, mode, this->ncidp); |
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72 | |
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73 | this->appendMode = true; |
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74 | // Find out how many temporal records have been written already to the file we are opening |
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75 | int ncUnlimitedDimId; |
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76 | CNetCdfInterface::inqUnLimDim(this->ncidp, ncUnlimitedDimId); |
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77 | if (ncUnlimitedDimId != -1) |
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78 | CNetCdfInterface::inqDimLen(this->ncidp, ncUnlimitedDimId, this->recordOffset); |
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79 | else |
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80 | this->recordOffset = 0; |
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81 | } |
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82 | |
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83 | // If the classic NetCDF format is used, we enable the "no-fill mode" globally. |
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84 | // This is done per variable for the NetCDF4 format. |
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85 | if (useClassicFormat) |
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86 | CNetCdfInterface::setFill(this->ncidp, false); |
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87 | } |
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88 | |
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89 | void CONetCDF4::close() |
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90 | { |
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91 | (CNetCdfInterface::close(this->ncidp)); |
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92 | } |
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93 | |
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94 | //--------------------------------------------------------------- |
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95 | |
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96 | void CONetCDF4::definition_start(void) |
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97 | { |
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98 | (CNetCdfInterface::reDef(this->ncidp)); |
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99 | } |
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100 | |
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101 | //--------------------------------------------------------------- |
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102 | |
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103 | void CONetCDF4::definition_end(void) |
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104 | { |
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105 | (CNetCdfInterface::endDef(this->ncidp)); |
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106 | } |
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107 | |
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108 | //--------------------------------------------------------------- |
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109 | |
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110 | // Don't need it anymore? |
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111 | // void CONetCDF4::CheckError(int status) |
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112 | // { |
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113 | // if (status != NC_NOERR) |
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114 | // { |
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115 | // StdString errormsg (nc_strerror(status)); // fuite mémoire ici ? |
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116 | // ERROR("CONetCDF4::CheckError(int status)", |
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117 | // << "[ status = " << status << " ] " << errormsg); |
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118 | // } |
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119 | // } |
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120 | |
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121 | //--------------------------------------------------------------- |
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122 | |
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123 | int CONetCDF4::getCurrentGroup(void) |
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124 | { |
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125 | return (this->getGroup(this->getCurrentPath())); |
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126 | } |
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127 | |
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128 | //--------------------------------------------------------------- |
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129 | |
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130 | int CONetCDF4::getGroup(const CONetCDF4Path & path) |
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131 | { |
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132 | int retvalue = this->ncidp; |
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133 | |
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134 | CONetCDF4Path::const_iterator |
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135 | it = path.begin(), end = path.end(); |
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136 | |
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137 | for (;it != end; it++) |
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138 | { |
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139 | const StdString & groupid = *it; |
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140 | (CNetCdfInterface::inqNcId(retvalue, groupid, retvalue)); |
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141 | } |
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142 | return (retvalue); |
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143 | } |
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144 | |
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145 | //--------------------------------------------------------------- |
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146 | |
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147 | int CONetCDF4::getVariable(const StdString & varname) |
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148 | { |
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149 | int varid = 0; |
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150 | int grpid = this->getCurrentGroup(); |
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151 | (CNetCdfInterface::inqVarId(grpid, varname, varid)); |
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152 | return (varid); |
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153 | } |
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154 | |
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155 | //--------------------------------------------------------------- |
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156 | |
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157 | int CONetCDF4::getDimension(const StdString & dimname) |
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158 | { |
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159 | int dimid = 0; |
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160 | int grpid = this->getCurrentGroup(); |
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161 | (CNetCdfInterface::inqDimId(grpid, dimname, dimid)); |
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162 | return (dimid); |
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163 | } |
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164 | |
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165 | //--------------------------------------------------------------- |
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166 | |
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167 | int CONetCDF4::getUnlimitedDimension(void) |
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168 | { |
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169 | int dimid = 0; |
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170 | int grpid = this->getCurrentGroup(); |
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171 | (CNetCdfInterface::inqUnLimDim(grpid, dimid)); |
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172 | return (dimid); |
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173 | } |
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174 | |
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175 | StdString CONetCDF4::getUnlimitedDimensionName(void) |
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176 | { |
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177 | int grpid = this->getGroup(path); |
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178 | int dimid = this->getUnlimitedDimension(); |
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179 | |
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180 | if (dimid == -1) return (std::string()); |
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181 | StdString dimname; |
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182 | (CNetCdfInterface::inqDimName(grpid, dimid, dimname)); |
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183 | |
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184 | return (dimname); |
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185 | } |
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186 | |
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187 | //--------------------------------------------------------------- |
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188 | |
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189 | std::vector<StdSize> CONetCDF4::getDimensions(const StdString & varname) |
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190 | { |
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191 | StdSize size = 0; |
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192 | std::vector<StdSize> retvalue; |
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193 | int grpid = this->getCurrentGroup(); |
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194 | int varid = this->getVariable(varname); |
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195 | int nbdim = 0, *dimid = NULL; |
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196 | |
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197 | (CNetCdfInterface::inqVarNDims(grpid, varid, nbdim)); |
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198 | dimid = new int[nbdim](); |
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199 | (CNetCdfInterface::inqVarDimId(grpid, varid, dimid)); |
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200 | |
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201 | for (int i = 0; i < nbdim; i++) |
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202 | { |
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203 | (CNetCdfInterface::inqDimLen(grpid, dimid[i], size)); |
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204 | if (size == NC_UNLIMITED) |
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205 | size = UNLIMITED_DIM; |
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206 | retvalue.push_back(size); |
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207 | } |
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208 | delete [] dimid; |
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209 | return (retvalue); |
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210 | } |
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211 | |
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212 | std::vector<std::string> CONetCDF4::getDimensionsIdList (const std::string * _varname) |
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213 | { |
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214 | int nDimNull = 0; |
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215 | int nbdim = 0, *dimid = NULL; |
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216 | int grpid = this->getCurrentGroup(); |
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217 | int varid = (_varname != NULL) ? this->getVariable(*_varname) : NC_GLOBAL; |
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218 | std::vector<std::string> retvalue; |
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219 | |
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220 | if (_varname != NULL) |
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221 | { |
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222 | (CNetCdfInterface::inqVarNDims(grpid, varid, nbdim)); |
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223 | dimid = new int[nbdim](); |
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224 | (CNetCdfInterface::inqVarDimId(grpid, varid, dimid)); |
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225 | } |
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226 | else |
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227 | { |
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228 | (CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1)); |
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229 | dimid = new int[nbdim](); |
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230 | (CNetCdfInterface::inqDimIds(grpid, nDimNull, dimid, 1)); |
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231 | } |
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232 | |
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233 | for (int i = 0; i < nbdim; i++) |
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234 | { |
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235 | std::string dimname; |
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236 | (CNetCdfInterface::inqDimName(grpid, dimid[i], dimname)); |
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237 | retvalue.push_back(dimname); |
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238 | } |
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239 | delete [] dimid; |
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240 | |
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241 | return (retvalue); |
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242 | } |
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243 | |
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244 | |
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245 | //--------------------------------------------------------------- |
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246 | |
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247 | const CONetCDF4::CONetCDF4Path & CONetCDF4::getCurrentPath(void) const |
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248 | { return (this->path); } |
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249 | |
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250 | void CONetCDF4::setCurrentPath(const CONetCDF4Path & path) |
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251 | { this->path = path; } |
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252 | |
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253 | //--------------------------------------------------------------- |
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254 | |
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255 | int CONetCDF4::addGroup(const StdString & name) |
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256 | { |
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257 | int retvalue = 0; |
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258 | int grpid = this->getCurrentGroup(); |
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259 | (CNetCdfInterface::defGrp(grpid, name, retvalue)); |
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260 | return (retvalue); |
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261 | } |
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262 | |
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263 | //--------------------------------------------------------------- |
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264 | |
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265 | int CONetCDF4::addDimension(const StdString& name, const StdSize size) |
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266 | { |
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267 | int retvalue = 0; |
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268 | int grpid = this->getCurrentGroup(); |
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269 | if (size != UNLIMITED_DIM) |
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270 | (CNetCdfInterface::defDim(grpid, name, size, retvalue)); |
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271 | else |
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272 | (CNetCdfInterface::defDim(grpid, name, NC_UNLIMITED, retvalue)); |
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273 | return (retvalue); |
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274 | } |
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275 | |
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276 | //--------------------------------------------------------------- |
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277 | |
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278 | int CONetCDF4::addVariable(const StdString & name, nc_type type, |
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279 | const std::vector<StdString> & dim) |
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280 | { |
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281 | int varid = 0; |
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282 | std::vector<int> dimids; |
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283 | std::vector<StdSize> dimsizes; |
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284 | StdSize size; |
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285 | StdSize totalSize; |
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286 | StdSize maxSize = 1024 * 1024 * 256; // == 2GB/8 if output double |
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287 | |
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288 | int grpid = this->getCurrentGroup(); |
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289 | |
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290 | std::vector<StdString>::const_iterator it = dim.begin(), end = dim.end(); |
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291 | |
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292 | for (; it != end; it++) |
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293 | { |
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294 | const StdString & dimid = *it; |
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295 | dimids.push_back(this->getDimension(dimid)); |
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296 | CNetCdfInterface::inqDimLen(grpid, this->getDimension(dimid), size); |
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297 | if (size == NC_UNLIMITED) size = 1; |
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298 | dimsizes.push_back(size); |
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299 | } |
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300 | |
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301 | CNetCdfInterface::defVar(grpid, name, type, dimids.size(), &dimids[0], varid); |
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302 | |
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303 | // The classic NetCDF format does not support chunking nor fill parameters |
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304 | if (!useClassicFormat) |
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305 | { |
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306 | // set chunksize : size of one record |
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307 | // but must not be > 2GB (netcdf or HDF5 problem) |
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308 | totalSize = 1; |
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309 | for (vector<StdSize>::reverse_iterator it = dimsizes.rbegin(); it != dimsizes.rend(); ++it) |
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310 | { |
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311 | totalSize *= *it; |
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312 | if (totalSize >= maxSize) *it = 1; |
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313 | } |
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314 | |
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315 | CNetCdfInterface::defVarChunking(grpid, varid, NC_CHUNKED, &dimsizes[0]); |
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316 | CNetCdfInterface::defVarFill(grpid, varid, true, NULL); |
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317 | } |
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318 | |
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319 | return varid; |
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320 | } |
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321 | |
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322 | //--------------------------------------------------------------- |
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323 | |
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324 | void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel) |
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325 | { |
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326 | if (compressionLevel < 0 || compressionLevel > 9) |
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327 | ERROR("void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel)", |
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328 | "Invalid compression level for variable \"" << varname << "\", the value should range between 0 and 9."); |
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329 | if (compressionLevel && wmpi) |
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330 | ERROR("void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel)", |
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331 | "Impossible to use compression for variable \"" << varname << "\" when using parallel mode."); |
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332 | |
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333 | int grpid = this->getCurrentGroup(); |
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334 | int varid = this->getVariable(varname); |
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335 | CNetCdfInterface::defVarDeflate(grpid, varid, compressionLevel); |
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336 | } |
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337 | |
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338 | //--------------------------------------------------------------- |
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339 | |
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340 | template <> |
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341 | void CONetCDF4::addAttribute |
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342 | (const StdString & name, const StdString & value, const StdString * varname ) |
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343 | { |
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344 | int grpid = this->getCurrentGroup(); |
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345 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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346 | (CNetCdfInterface::putAtt(grpid, varid, name, NC_CHAR, value.size(), value.c_str())); |
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347 | //CheckError(nc_put_att_string(grpid, varid, name.c_str(), 1, &str)); |
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348 | } |
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349 | |
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350 | //--------------------------------------------------------------- |
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351 | |
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352 | template <> |
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353 | void CONetCDF4::addAttribute |
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354 | (const StdString & name, const double & value, const StdString * varname ) |
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355 | { |
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356 | int grpid = this->getCurrentGroup(); |
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357 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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358 | (CNetCdfInterface::putAttType(grpid, varid, name, 1, &value)); |
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359 | } |
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360 | |
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361 | template <> |
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362 | void CONetCDF4::addAttribute |
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363 | (const StdString & name, const CArray<double,1>& value, const StdString * varname ) |
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364 | { |
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365 | int grpid = this->getCurrentGroup(); |
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366 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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367 | (CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst())); |
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368 | } |
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369 | //--------------------------------------------------------------- |
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370 | |
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371 | template <> |
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372 | void CONetCDF4::addAttribute |
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373 | (const StdString & name, const float & value, const StdString * varname ) |
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374 | { |
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375 | int grpid = this->getCurrentGroup(); |
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376 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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377 | (CNetCdfInterface::putAttType(grpid, varid, name, 1, &value)); |
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378 | } |
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379 | |
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380 | template <> |
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381 | void CONetCDF4::addAttribute |
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382 | (const StdString & name, const CArray<float,1>& value, const StdString * varname ) |
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383 | { |
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384 | int grpid = this->getCurrentGroup(); |
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385 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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386 | (CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst())); |
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387 | } |
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388 | |
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389 | //--------------------------------------------------------------- |
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390 | |
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391 | template <> |
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392 | void CONetCDF4::addAttribute |
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393 | (const StdString & name, const int & value, const StdString * varname ) |
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394 | { |
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395 | int grpid = this->getCurrentGroup(); |
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396 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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397 | (CNetCdfInterface::putAttType(grpid, varid, name, 1, &value)); |
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398 | } |
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399 | |
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400 | template <> |
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401 | void CONetCDF4::addAttribute |
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402 | (const StdString & name, const CArray<int,1>& value, const StdString * varname ) |
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403 | { |
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404 | int grpid = this->getCurrentGroup(); |
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405 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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406 | (CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst())); |
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407 | } |
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408 | |
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409 | template <> |
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410 | void CONetCDF4::addAttribute |
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411 | (const StdString & name, const short int & value, const StdString * varname ) |
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412 | { |
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413 | int grpid = this->getCurrentGroup(); |
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414 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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415 | (CNetCdfInterface::putAttType(grpid, varid, name, 1, &value)); |
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416 | } |
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417 | |
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418 | template <> |
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419 | void CONetCDF4::addAttribute |
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420 | (const StdString & name, const CArray<short int,1>& value, const StdString * varname ) |
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421 | { |
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422 | int grpid = this->getCurrentGroup(); |
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423 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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424 | (CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst())); |
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425 | } |
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426 | |
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427 | |
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428 | |
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429 | template <> |
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430 | void CONetCDF4::addAttribute |
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431 | (const StdString & name, const long int & value, const StdString * varname ) |
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432 | { |
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433 | int grpid = this->getCurrentGroup(); |
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434 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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435 | (CNetCdfInterface::putAttType(grpid, varid, name, 1, &value)); |
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436 | } |
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437 | |
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438 | template <> |
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439 | void CONetCDF4::addAttribute |
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440 | (const StdString & name, const CArray<long int,1>& value, const StdString * varname ) |
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441 | { |
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442 | int grpid = this->getCurrentGroup(); |
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443 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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444 | (CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst())); |
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445 | } |
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446 | |
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447 | |
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448 | |
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449 | //--------------------------------------------------------------- |
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450 | |
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451 | void CONetCDF4::getWriteDataInfos(const StdString & name, StdSize record, StdSize & array_size, |
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452 | std::vector<StdSize> & sstart, |
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453 | std::vector<StdSize> & scount, |
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454 | const std::vector<StdSize> * start, |
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455 | const std::vector<StdSize> * count) |
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456 | { |
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457 | std::vector<std::size_t> sizes = this->getDimensions(name); |
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458 | std::vector<std::string> iddims = this->getDimensionsIdList (&name); |
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459 | std::vector<std::size_t>::const_iterator |
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460 | it = sizes.begin(), end = sizes.end(); |
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461 | int i = 0; |
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462 | |
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463 | if (iddims.begin()->compare(this->getUnlimitedDimensionName()) == 0) |
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464 | { |
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465 | sstart.push_back(record + recordOffset); |
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466 | scount.push_back(1); |
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467 | if ((start == NULL) && |
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468 | (count == NULL)) i++; |
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469 | it++; |
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470 | } |
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471 | |
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472 | for (;it != end; it++) |
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473 | { |
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474 | if ((start != NULL) && (count != NULL)) |
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475 | { |
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476 | sstart.push_back((*start)[i]); |
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477 | scount.push_back((*count)[i]); |
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478 | array_size *= (*count)[i]; |
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479 | i++; |
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480 | } |
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481 | else |
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482 | { |
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483 | sstart.push_back(0); |
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484 | scount.push_back(sizes[i]); |
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485 | array_size *= sizes[i]; |
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486 | i++; |
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487 | } |
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488 | } |
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489 | |
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490 | } |
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491 | |
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492 | |
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493 | |
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494 | template <> |
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495 | void CONetCDF4::writeData_(int grpid, int varid, |
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496 | const std::vector<StdSize> & sstart, |
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497 | const std::vector<StdSize> & scount, const double * data) |
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498 | { |
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499 | (CNetCdfInterface::putVaraType(grpid, varid, &(sstart[0]), &(scount[0]), data)); |
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500 | // sync() ; |
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501 | } |
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502 | |
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503 | //--------------------------------------------------------------- |
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504 | |
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505 | template <> |
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506 | void CONetCDF4::writeData_(int grpid, int varid, |
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507 | const std::vector<StdSize> & sstart, |
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508 | const std::vector<StdSize> & scount, const int * data) |
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509 | { |
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510 | (CNetCdfInterface::putVaraType(grpid, varid, &(sstart[0]), &(scount[0]), data)); |
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511 | // sync() ; |
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512 | } |
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513 | |
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514 | //--------------------------------------------------------------- |
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515 | |
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516 | template <> |
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517 | void CONetCDF4::writeData_(int grpid, int varid, |
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518 | const std::vector<StdSize> & sstart, |
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519 | const std::vector<StdSize> & scount, const float * data) |
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520 | { |
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521 | (CNetCdfInterface::putVaraType(grpid, varid, &(sstart[0]), &(scount[0]), data)); |
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522 | // sync() ; |
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523 | } |
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524 | |
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525 | //--------------------------------------------------------------- |
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526 | |
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527 | void CONetCDF4::writeData(const CArray<int, 2>& data, const StdString & name) |
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528 | { |
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529 | int grpid = this->getCurrentGroup(); |
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530 | int varid = this->getVariable(name); |
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531 | StdSize array_size = 1; |
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532 | std::vector<StdSize> sstart, scount; |
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533 | |
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534 | this->getWriteDataInfos(name, 0, array_size, sstart, scount, NULL, NULL); |
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535 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
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536 | } |
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537 | |
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538 | void CONetCDF4::writeTimeAxisData(const CArray<double, 1>& data, const StdString & name, |
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539 | bool collective, StdSize record, bool isRoot) |
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540 | { |
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541 | int grpid = this->getCurrentGroup(); |
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542 | int varid = this->getVariable(name); |
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543 | |
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544 | map<int,size_t>::iterator it=timeAxis.find(varid) ; |
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545 | if (it==timeAxis.end()) timeAxis[varid]=record ; |
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546 | else |
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547 | { |
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548 | if (it->second >= record) return ; |
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549 | else it->second =record ; |
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550 | } |
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551 | |
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552 | StdSize array_size = 1; |
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553 | std::vector<StdSize> sstart, scount; |
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554 | |
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555 | if (this->wmpi && collective) |
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556 | (CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE)); |
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557 | if (this->wmpi && !collective) |
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558 | (CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT)); |
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559 | |
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560 | this->getWriteDataInfos(name, record, array_size, sstart, scount, NULL, NULL); |
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561 | if (using_netcdf_internal) if (!isRoot) { sstart[0]=sstart[0]+1 ; scount[0]=0 ;} |
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562 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
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563 | } |
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564 | |
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565 | //--------------------------------------------------------------- |
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566 | |
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567 | bool CONetCDF4::varExist(const StdString & varname) |
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568 | { |
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569 | int grpid = this->getCurrentGroup(); |
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570 | return (CNetCdfInterface::isVarExisted(grpid, varname)); |
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571 | } |
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572 | |
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573 | void CONetCDF4::sync(void) |
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574 | { |
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575 | (CNetCdfInterface::sync(this->ncidp)) ; |
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576 | } |
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577 | ///-------------------------------------------------------------- |
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578 | } // namespace xios |
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