1 | #include "file.hpp" |
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2 | |
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3 | #include "attribute_template.hpp" |
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4 | #include "object_template.hpp" |
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5 | #include "group_template.hpp" |
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6 | #include "object_factory.hpp" |
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7 | #include "context.hpp" |
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8 | #include "context_server.hpp" |
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9 | #include "nc4_data_output.hpp" |
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10 | #include "nc4_data_input.hpp" |
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11 | #include "calendar_util.hpp" |
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12 | #include "date.hpp" |
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13 | #include "message.hpp" |
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14 | #include "type.hpp" |
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15 | #include "xios_spl.hpp" |
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16 | #include "context_client.hpp" |
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17 | #include "mpi.hpp" |
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18 | #include "timer.hpp" |
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19 | |
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20 | namespace xios { |
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21 | |
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22 | /// ////////////////////// Dfinitions ////////////////////// /// |
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23 | |
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24 | CFile::CFile(void) |
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25 | : CObjectTemplate<CFile>(), CFileAttributes() |
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26 | , vFieldGroup(), data_out(), enabledFields(), fileComm(MPI_COMM_NULL) |
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27 | , allDomainEmpty(false), isOpen(false) |
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28 | { |
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29 | setVirtualFieldGroup(CFieldGroup::create(getId() + "_virtual_field_group")); |
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30 | setVirtualVariableGroup(CVariableGroup::create(getId() + "_virtual_variable_group")); |
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31 | } |
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32 | |
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33 | CFile::CFile(const StdString & id) |
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34 | : CObjectTemplate<CFile>(id), CFileAttributes() |
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35 | , vFieldGroup(), data_out(), enabledFields(), fileComm(MPI_COMM_NULL) |
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36 | , allDomainEmpty(false), isOpen(false) |
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37 | { |
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38 | setVirtualFieldGroup(CFieldGroup::create(getId() + "_virtual_field_group")); |
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39 | setVirtualVariableGroup(CVariableGroup::create(getId() + "_virtual_variable_group")); |
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40 | } |
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41 | |
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42 | CFile::~CFile(void) |
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43 | { /* Ne rien faire de plus */ } |
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44 | |
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45 | ///--------------------------------------------------------------- |
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46 | //! Get name of file |
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47 | StdString CFile::GetName(void) { return (StdString("file")); } |
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48 | StdString CFile::GetDefName(void){ return (CFile::GetName()); } |
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49 | ENodeType CFile::GetType(void) { return (eFile); } |
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50 | |
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51 | //---------------------------------------------------------------- |
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52 | |
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53 | const StdString CFile::getFileOutputName(void) const |
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54 | { |
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55 | return (name.isEmpty() ? getId() : name) + (name_suffix.isEmpty() ? StdString("") : name_suffix.getValue()); |
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56 | } |
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57 | |
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58 | //---------------------------------------------------------------- |
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59 | /*! |
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60 | \brief Get data writer object. |
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61 | Each enabled file in xml represents a physical netcdf file. |
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62 | This function allows to access the data writer object. |
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63 | \return data writer object. |
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64 | */ |
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65 | boost::shared_ptr<CDataOutput> CFile::getDataOutput(void) const |
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66 | { |
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67 | return data_out; |
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68 | } |
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69 | |
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70 | /*! |
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71 | \brief Get data reader object. |
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72 | Each enabled file in xml represents a physical netcdf file. |
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73 | This function allows to access the data reader object. |
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74 | \return data reader object. |
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75 | */ |
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76 | boost::shared_ptr<CDataInput> CFile::getDataInput(void) const |
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77 | { |
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78 | return data_in; |
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79 | } |
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80 | |
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81 | /*! |
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82 | \brief Get virtual field group |
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83 | In each file, there always exists a field group which is the ancestor of all |
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84 | fields in the file. This is considered be virtual because it is created automatically during |
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85 | file initialization and it normally doesn't appear on xml file |
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86 | \return Pointer to field group |
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87 | */ |
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88 | CFieldGroup* CFile::getVirtualFieldGroup(void) const |
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89 | { |
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90 | return (this->vFieldGroup); |
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91 | } |
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92 | |
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93 | /*! |
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94 | \brief Get virtual variable group |
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95 | In each file, there always exists a variable group which is the ancestor of all |
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96 | variable in the file. This is considered be virtual because it is created automatically during |
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97 | file initialization and it normally doesn't appear on xml file |
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98 | \return Pointer to variable group |
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99 | */ |
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100 | CVariableGroup* CFile::getVirtualVariableGroup(void) const |
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101 | { |
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102 | return (this->vVariableGroup); |
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103 | } |
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104 | |
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105 | //! Get all fields of a file |
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106 | std::vector<CField*> CFile::getAllFields(void) const |
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107 | { |
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108 | return (this->vFieldGroup->getAllChildren()); |
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109 | } |
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110 | |
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111 | //! Get all variables of a file |
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112 | std::vector<CVariable*> CFile::getAllVariables(void) const |
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113 | { |
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114 | return (this->vVariableGroup->getAllChildren()); |
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115 | } |
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116 | |
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117 | //---------------------------------------------------------------- |
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118 | /*! |
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119 | \brief Get all enabled fields of file |
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120 | A field is considered to be enabled if it fullfil these conditions: it is enabled, inside a enabled file |
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121 | and its own level is not larger than file output level. |
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122 | \param [in] default_outputlevel default value output level of file |
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123 | \param [in] default_level default value level of field |
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124 | \param [in] default_enabled flag determine by default if field is enabled |
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125 | \return Vector of pointers of enabled fields |
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126 | */ |
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127 | std::vector<CField*> CFile::getEnabledFields(int default_outputlevel, |
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128 | int default_level, |
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129 | bool default_enabled) |
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130 | { |
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131 | if (!this->enabledFields.empty()) |
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132 | return (this->enabledFields); |
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133 | |
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134 | const int _outputlevel = |
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135 | (!output_level.isEmpty()) ? output_level.getValue() : default_outputlevel; |
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136 | std::vector<CField*>::iterator it; |
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137 | this->enabledFields = this->getAllFields(); |
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138 | |
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139 | std::vector<CField*> newEnabledFields; |
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140 | |
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141 | for ( it = this->enabledFields.begin(); it != this->enabledFields.end(); it++ ) |
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142 | { |
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143 | if (!(*it)->enabled.isEmpty()) // Si l'attribut 'enabled' est dfini ... |
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144 | { |
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145 | if (! (*it)->enabled.getValue()) continue; |
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146 | // { it--; this->enabledFields.erase(it+1); continue; } |
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147 | } |
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148 | else // Si l'attribut 'enabled' n'est pas dfini ... |
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149 | { |
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150 | if (!default_enabled) continue; |
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151 | // { it--; this->enabledFields.erase(it+1); continue; } |
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152 | } |
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153 | |
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154 | if (!(*it)->level.isEmpty()) // Si l'attribut 'level' est dfini ... |
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155 | { |
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156 | if ((*it)->level.getValue() > _outputlevel) continue; |
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157 | // { it--; this->enabledFields.erase(it+1); continue; } |
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158 | } |
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159 | else // Si l'attribut 'level' n'est pas dfini ... |
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160 | { |
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161 | if (default_level > _outputlevel) continue; |
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162 | // { it--; this->enabledFields.erase(it+1); continue; } |
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163 | } |
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164 | |
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165 | // CField* field_tmp=(*it).get(); |
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166 | // shared_ptr<CField> sptfield=*it; |
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167 | // field_tmp->refObject.push_back(sptfield); |
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168 | newEnabledFields.push_back(*it); |
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169 | // Le champ est finalement actif, on y ajoute sa propre reference. |
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170 | // (*it)->refObject.push_back(*it); |
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171 | // Le champ est finalement actif, on y ajoute la rfrence au champ de base. |
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172 | (*it)->setRelFile(CFile::get(this)); |
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173 | } |
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174 | enabledFields = newEnabledFields; |
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175 | |
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176 | return (this->enabledFields); |
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177 | } |
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178 | |
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179 | //---------------------------------------------------------------- |
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180 | //! Change virtual field group to a new one |
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181 | void CFile::setVirtualFieldGroup(CFieldGroup* newVFieldGroup) |
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182 | { |
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183 | this->vFieldGroup = newVFieldGroup; |
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184 | } |
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185 | |
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186 | //! Change virtual variable group to new one |
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187 | void CFile::setVirtualVariableGroup(CVariableGroup* newVVariableGroup) |
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188 | { |
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189 | this->vVariableGroup = newVVariableGroup; |
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190 | } |
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191 | |
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192 | //---------------------------------------------------------------- |
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193 | bool CFile::isSyncTime(void) |
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194 | { |
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195 | CContext* context = CContext::getCurrent(); |
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196 | const CDate& currentDate = context->calendar->getCurrentDate(); |
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197 | if (!sync_freq.isEmpty()) |
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198 | { |
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199 | if (lastSync + sync_freq.getValue() < currentDate) |
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200 | { |
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201 | lastSync = currentDate; |
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202 | return true; |
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203 | } |
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204 | } |
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205 | return false; |
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206 | } |
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207 | |
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208 | //! Initialize a file in order to write into it |
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209 | void CFile::initFile(void) |
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210 | { |
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211 | CContext* context = CContext::getCurrent(); |
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212 | const CDate& currentDate = context->calendar->getCurrentDate(); |
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213 | CContextServer* server = context->server; |
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214 | |
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215 | lastSync = currentDate; |
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216 | lastSplit = currentDate; |
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217 | if (!split_freq.isEmpty()) |
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218 | { |
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219 | StdString keySuffix("CContext_"+CContext::getCurrent()->getId()+"::CFile_"+getFileOutputName()+"::") ; |
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220 | if (context->registryIn->foundKey(keySuffix+"splitStart") && context->registryIn->foundKey(keySuffix+"splitEnd")) |
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221 | { |
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222 | CDate savedSplitStart(*context->getCalendar()), savedSplitEnd(*context->getCalendar()); |
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223 | context->registryIn->getKey(keySuffix+"splitStart", savedSplitStart); |
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224 | context->registryIn->getKey(keySuffix+"splitEnd", savedSplitEnd); |
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225 | |
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226 | if (savedSplitStart <= lastSplit && lastSplit <= savedSplitEnd) |
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227 | lastSplit = savedSplitStart; |
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228 | } |
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229 | } |
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230 | isOpen = false; |
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231 | |
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232 | allDomainEmpty = true; |
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233 | |
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234 | // if (!record_offset.isEmpty() && record_offset < 0) |
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235 | // ERROR("void CFile::initFile(void)", |
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236 | // "Invalid 'record_offset', this attribute cannot be negative."); |
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237 | const int recordOffset = record_offset.isEmpty() ? 0 : record_offset; |
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238 | |
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239 | set<StdString> setAxis; |
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240 | set<StdString> setDomains; |
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241 | |
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242 | std::vector<CField*>::iterator it, end = this->enabledFields.end(); |
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243 | for (it = this->enabledFields.begin(); it != end; it++) |
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244 | { |
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245 | CField* field = *it; |
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246 | allDomainEmpty &= !field->grid->doGridHaveDataToWrite(); |
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247 | std::vector<CAxis*> vecAxis = field->grid->getAxis(); |
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248 | for (size_t i = 0; i < vecAxis.size(); ++i) |
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249 | setAxis.insert(vecAxis[i]->getAxisOutputName()); |
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250 | // setAxis.insert(vecAxis[i]); |
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251 | std::vector<CDomain*> vecDomains = field->grid->getDomains(); |
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252 | for (size_t i = 0; i < vecDomains.size(); ++i) |
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253 | setDomains.insert(vecDomains[i]->getDomainOutputName()); |
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254 | // setDomains.insert(vecDomains[i]); |
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255 | |
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256 | field->resetNStep(recordOffset); |
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257 | } |
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258 | nbAxis = setAxis.size(); |
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259 | nbDomains = setDomains.size(); |
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260 | |
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261 | // create sub communicator for file |
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262 | int color = allDomainEmpty ? 0 : 1; |
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263 | MPI_Comm_split(server->intraComm, color, server->intraCommRank, &fileComm); |
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264 | if (allDomainEmpty) MPI_Comm_free(&fileComm); |
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265 | |
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266 | // if (time_counter.isEmpty()) time_counter.setValue(time_counter_attr::centered); |
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267 | if (time_counter_name.isEmpty()) time_counter_name = "time_counter"; |
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268 | } |
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269 | |
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270 | /* |
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271 | Check condition to write into a file |
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272 | For now, we only use the level-2 server to write files (if this mode is activated) |
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273 | or classical server to do this job. |
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274 | */ |
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275 | void CFile::checkWriteFile(void) |
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276 | { |
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277 | CContext* context = CContext::getCurrent(); |
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278 | // Done by classical server or secondary server |
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279 | // This condition should be changed soon |
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280 | if (!CXios::usingServer2 || (CXios::usingServer2 && !context->hasClient)) |
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281 | { |
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282 | if (mode.isEmpty() || mode.getValue() == mode_attr::write) |
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283 | { |
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284 | CTimer::get("Files : create headers").resume(); |
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285 | if (!isOpen) createHeader(); |
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286 | CTimer::get("Files : create headers").suspend(); |
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287 | checkSync(); |
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288 | } |
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289 | checkSplit(); // REally need this? |
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290 | } |
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291 | } |
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292 | |
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293 | /* |
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294 | Check condition to read from a file |
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295 | For now, we only use the level-1 server to write files (if this mode is activated) |
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296 | or classical server to do this job. |
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297 | This function can be used by client for reading metadata |
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298 | */ |
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299 | void CFile::checkReadFile(void) |
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300 | { |
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301 | CContext* context = CContext::getCurrent(); |
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302 | // Done by classical server or secondary server |
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303 | // TODO: This condition should be changed soon. It only works with maximum number of level as 2 |
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304 | if (!CXios::usingServer2 || (CXios::usingServer2 && context->hasClient)) |
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305 | { |
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306 | if (!mode.isEmpty() && mode.getValue() == mode_attr::read) |
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307 | { |
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308 | CTimer::get("Files : open headers").resume(); |
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309 | if (!isOpen) openInReadMode(&(context->server->intraComm)); |
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310 | CTimer::get("Files : open headers").suspend(); |
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311 | } |
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312 | //checkSplit(); // Really need for reading? |
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313 | } |
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314 | } |
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315 | |
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316 | /*! |
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317 | \brief Verify if synchronisation should be done |
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318 | If syn option is enabled, syn frequence and current time will be used to |
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319 | calculate the moment to syn file(s) |
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320 | \return True if it is the moment to synchronize file, otherwise false |
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321 | */ |
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322 | bool CFile::checkSync(void) |
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323 | { |
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324 | CContext* context = CContext::getCurrent(); |
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325 | const CDate& currentDate = context->calendar->getCurrentDate(); |
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326 | if (!sync_freq.isEmpty()) |
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327 | { |
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328 | if (lastSync + sync_freq.getValue() <= currentDate) |
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329 | { |
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330 | lastSync = currentDate; |
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331 | data_out->syncFile(); |
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332 | return true; |
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333 | } |
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334 | } |
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335 | return false; |
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336 | } |
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337 | |
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338 | /*! |
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339 | \brief Verify if splitting should be done |
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340 | If split option is enabled, split frequence and current time will be used to |
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341 | calculate the moment to split file |
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342 | \return True if it is the moment to split file, otherwise false |
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343 | */ |
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344 | bool CFile::checkSplit(void) |
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345 | { |
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346 | CContext* context = CContext::getCurrent(); |
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347 | const CDate& currentDate = context->calendar->getCurrentDate(); |
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348 | if (!split_freq.isEmpty()) |
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349 | { |
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350 | if (currentDate > lastSplit + split_freq.getValue()) |
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351 | { |
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352 | lastSplit = lastSplit + split_freq.getValue(); |
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353 | std::vector<CField*>::iterator it, end = this->enabledFields.end(); |
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354 | for (it = this->enabledFields.begin(); it != end; it++) |
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355 | { |
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356 | (*it)->resetNStep(); |
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357 | (*it)->resetNStepMax(); |
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358 | } |
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359 | if (mode.isEmpty() || mode.getValue() == mode_attr::write) |
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360 | createHeader(); |
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361 | else |
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362 | openInReadMode(); |
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363 | return true; |
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364 | } |
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365 | } |
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366 | return false; |
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367 | } |
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368 | |
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369 | /*! |
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370 | \brief Create header of netcdf file |
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371 | There are some information to fill in header of each netcdf. |
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372 | */ |
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373 | void CFile::createHeader(void) |
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374 | { |
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375 | CContext* context = CContext::getCurrent(); |
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376 | CContextServer* server = context->server; |
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377 | |
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378 | if (!allDomainEmpty) |
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379 | { |
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380 | StdString filename = getFileOutputName(); |
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381 | |
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382 | // determine splitting format in the file name : firstPart%start_date%middlePart%end_date%lastPart |
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383 | |
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384 | std::string strStartDate="%start_date%" ; |
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385 | std::string strEndDate="%end_date%" ; |
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386 | |
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387 | std::string firstPart ; |
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388 | std::string middlePart ; |
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389 | std::string lastPart ; |
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390 | size_t pos1, pos2 ; |
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391 | bool hasStartDate=false ; |
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392 | bool hasEndDate=false ; |
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393 | bool hasSplit = (!split_freq.isEmpty()); |
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394 | |
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395 | pos1=filename.find(strStartDate) ; |
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396 | if (pos1!=std::string::npos) |
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397 | { |
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398 | firstPart=filename.substr(0,pos1) ; |
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399 | pos1+=strStartDate.size() ; |
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400 | hasStartDate=true ; |
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401 | } |
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402 | else pos1=0 ; |
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403 | |
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404 | pos2=filename.find(strEndDate,pos1) ; |
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405 | if (pos2!=std::string::npos) |
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406 | { |
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407 | middlePart=filename.substr(pos1,pos2-pos1) ; |
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408 | pos2+=strEndDate.size() ; |
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409 | lastPart=filename.substr(pos2,filename.size()-pos2) ; |
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410 | hasEndDate=true ; |
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411 | } |
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412 | else middlePart=filename.substr(pos1,filename.size()) ; |
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413 | |
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414 | if (!hasStartDate && !hasEndDate) |
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415 | { |
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416 | hasStartDate=true ; |
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417 | hasEndDate=true; |
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418 | firstPart=middlePart ; |
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419 | if (hasSplit) firstPart +="_"; |
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420 | middlePart="-" ; |
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421 | } |
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422 | |
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423 | StdOStringStream oss; |
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424 | |
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425 | if (!split_freq.isEmpty()) |
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426 | { |
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427 | CDate split_start ; |
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428 | CDate splitEnd ; |
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429 | if (!split_start_offset.isEmpty()) split_start=lastSplit + split_start_offset ; |
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430 | else split_start=lastSplit ; |
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431 | |
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432 | splitEnd = lastSplit + split_freq ; |
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433 | if (!split_last_date.isEmpty()) |
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434 | { |
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435 | CDate splitLastDate=CDate::FromString(split_last_date,*CContext::getCurrent()->getCalendar()) ; |
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436 | if( splitLastDate < splitEnd) splitEnd=splitLastDate ; |
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437 | } |
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438 | |
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439 | if (!split_end_offset.isEmpty()) splitEnd = splitEnd + split_end_offset; |
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440 | else splitEnd = splitEnd - 1 * Second; |
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441 | |
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442 | string splitFormat; |
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443 | if (split_freq_format.isEmpty()) |
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444 | { |
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445 | if (split_freq.getValue().second != 0) splitFormat = "%y%mo%d%h%mi%s"; |
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446 | else if (split_freq.getValue().minute != 0) splitFormat = "%y%mo%d%h%mi"; |
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447 | else if (split_freq.getValue().hour != 0) splitFormat = "%y%mo%d%h"; |
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448 | else if (split_freq.getValue().day != 0) splitFormat = "%y%mo%d"; |
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449 | else if (split_freq.getValue().month != 0) splitFormat = "%y%mo"; |
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450 | else splitFormat = "%y"; |
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451 | } |
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452 | else splitFormat = split_freq_format; |
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453 | |
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454 | oss << firstPart ; |
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455 | if (hasStartDate) oss << split_start.getStr(splitFormat) ; |
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456 | oss << middlePart ; |
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457 | if (hasEndDate) oss << splitEnd.getStr(splitFormat); |
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458 | oss << lastPart ; |
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459 | |
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460 | StdString keySuffix("CContext_"+CContext::getCurrent()->getId()+"::CFile_"+getFileOutputName()+"::") ; |
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461 | context->registryOut->setKey(keySuffix+"splitStart", lastSplit); |
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462 | context->registryOut->setKey(keySuffix+"splitEnd", splitEnd); |
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463 | } |
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464 | else oss<<firstPart<<lastPart ; |
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465 | |
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466 | bool append = !this->append.isEmpty() && this->append.getValue(); |
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467 | |
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468 | bool useClassicFormat = !format.isEmpty() && format == format_attr::netcdf4_classic; |
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469 | bool useCFConvention = convention.isEmpty() || convention == convention_attr::CF; |
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470 | |
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471 | bool multifile = true; |
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472 | if (!type.isEmpty()) |
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473 | { |
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474 | if (type == type_attr::one_file) multifile = false; |
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475 | else if (type == type_attr::multiple_file) multifile = true; |
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476 | |
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477 | } |
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478 | #ifndef USING_NETCDF_PAR |
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479 | if (!multifile) |
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480 | { |
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481 | info(0) << "!!! Warning -> Using non parallel version of netcdf, switching in multiple_file mode for file : " << filename << " ..." << endl; |
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482 | multifile = true; |
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483 | } |
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484 | #endif |
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485 | if (multifile) |
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486 | { |
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487 | int commSize, commRank; |
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488 | MPI_Comm_size(fileComm, &commSize); |
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489 | MPI_Comm_rank(fileComm, &commRank); |
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490 | |
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491 | if (server->intraCommSize > 1) |
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492 | { |
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493 | oss << "_" ; |
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494 | int width=0; int n = commSize-1; |
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495 | while (n != 0) { n = n / 10; width++;} |
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496 | if (!min_digits.isEmpty()) |
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497 | if (width < min_digits) width = min_digits; |
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498 | oss.width(width); |
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499 | oss.fill('0'); |
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500 | oss << right << commRank; |
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501 | } |
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502 | } |
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503 | oss << ".nc"; |
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504 | |
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505 | bool isCollective = par_access.isEmpty() || par_access == par_access_attr::collective; |
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506 | |
---|
507 | if (isOpen) data_out->closeFile(); |
---|
508 | |
---|
509 | data_out = shared_ptr<CDataOutput>(new CNc4DataOutput(this, oss.str(), append, useClassicFormat, useCFConvention, |
---|
510 | fileComm, multifile, isCollective, time_counter_name)); |
---|
511 | isOpen = true; |
---|
512 | |
---|
513 | data_out->writeFile(CFile::get(this)); |
---|
514 | |
---|
515 | // Do not recreate the file structure if opening an existing file |
---|
516 | if (!data_out->IsInAppendMode()) |
---|
517 | { |
---|
518 | std::vector<CField*>::iterator it, end = this->enabledFields.end(); |
---|
519 | for (it = this->enabledFields.begin(); it != end; it++) |
---|
520 | { |
---|
521 | CField* field = *it; |
---|
522 | this->data_out->writeFieldGrid(field); |
---|
523 | } |
---|
524 | this->data_out->writeTimeDimension(); |
---|
525 | |
---|
526 | for (it = this->enabledFields.begin(); it != end; it++) |
---|
527 | { |
---|
528 | CField* field = *it; |
---|
529 | this->data_out->writeFieldTimeAxis(field); |
---|
530 | } |
---|
531 | |
---|
532 | for (it = this->enabledFields.begin(); it != end; it++) |
---|
533 | { |
---|
534 | CField* field = *it; |
---|
535 | this->data_out->writeField(field); |
---|
536 | } |
---|
537 | |
---|
538 | vector<CVariable*> listVars = getAllVariables(); |
---|
539 | for (vector<CVariable*>::iterator it = listVars.begin(); it != listVars.end(); it++) |
---|
540 | this->data_out->writeAttribute(*it); |
---|
541 | |
---|
542 | this->data_out->definition_end(); |
---|
543 | } |
---|
544 | else |
---|
545 | { |
---|
546 | // check time axis even in append mode |
---|
547 | std::vector<CField*>::iterator it, end = this->enabledFields.end(); |
---|
548 | for (it = this->enabledFields.begin(); it != end; it++) |
---|
549 | { |
---|
550 | CField* field = *it; |
---|
551 | this->data_out->writeFieldTimeAxis(field); |
---|
552 | } |
---|
553 | } |
---|
554 | } |
---|
555 | } |
---|
556 | |
---|
557 | /*! |
---|
558 | \brief Open an existing NetCDF file in read-only mode |
---|
559 | */ |
---|
560 | void CFile::openInReadMode(MPI_Comm* comm) |
---|
561 | { |
---|
562 | CContext* context = CContext::getCurrent(); |
---|
563 | CContextServer* server = context->server; |
---|
564 | MPI_Comm readComm = *comm; |
---|
565 | |
---|
566 | if (!allDomainEmpty) |
---|
567 | { |
---|
568 | StdString filename = getFileOutputName(); |
---|
569 | StdOStringStream oss; |
---|
570 | oss << filename; |
---|
571 | |
---|
572 | if (!split_freq.isEmpty()) |
---|
573 | { |
---|
574 | string splitFormat; |
---|
575 | if (split_freq_format.isEmpty()) |
---|
576 | { |
---|
577 | if (split_freq.getValue().second != 0) splitFormat = "%y%mo%d%h%mi%s"; |
---|
578 | else if (split_freq.getValue().minute != 0) splitFormat = "%y%mo%d%h%mi"; |
---|
579 | else if (split_freq.getValue().hour != 0) splitFormat = "%y%mo%d%h"; |
---|
580 | else if (split_freq.getValue().day != 0) splitFormat = "%y%mo%d"; |
---|
581 | else if (split_freq.getValue().month != 0) splitFormat = "%y%mo"; |
---|
582 | else splitFormat = "%y"; |
---|
583 | } |
---|
584 | else splitFormat = split_freq_format; |
---|
585 | oss << "_" << lastSplit.getStr(splitFormat) |
---|
586 | << "-" << (lastSplit + split_freq.getValue() - 1 * Second).getStr(splitFormat); |
---|
587 | } |
---|
588 | |
---|
589 | bool multifile = true; |
---|
590 | if (!type.isEmpty()) |
---|
591 | { |
---|
592 | if (type == type_attr::one_file) multifile = false; |
---|
593 | else if (type == type_attr::multiple_file) multifile = true; |
---|
594 | } |
---|
595 | #ifndef USING_NETCDF_PAR |
---|
596 | if (!multifile) |
---|
597 | { |
---|
598 | info(0) << "!!! Warning -> Using non parallel version of netcdf, switching in multiple_file mode for file : " << filename << " ..." << endl; |
---|
599 | multifile = true; |
---|
600 | } |
---|
601 | #endif |
---|
602 | if (multifile) |
---|
603 | { |
---|
604 | int commSize, commRank; |
---|
605 | MPI_Comm_size(readComm, &commSize); |
---|
606 | MPI_Comm_rank(readComm, &commRank); |
---|
607 | |
---|
608 | if (server->intraCommSize > 1) |
---|
609 | { |
---|
610 | oss << "_"; |
---|
611 | int width = 0, n = commSize - 1; |
---|
612 | while (n != 0) { n = n / 10; width++; } |
---|
613 | if (!min_digits.isEmpty() && width < min_digits) |
---|
614 | width = min_digits; |
---|
615 | oss.width(width); |
---|
616 | oss.fill('0'); |
---|
617 | oss << right << commRank; |
---|
618 | } |
---|
619 | } |
---|
620 | oss << ".nc"; |
---|
621 | |
---|
622 | bool isCollective = par_access.isEmpty() || par_access == par_access_attr::collective; |
---|
623 | |
---|
624 | if (isOpen) data_out->closeFile(); |
---|
625 | if (time_counter_name.isEmpty()) data_in = shared_ptr<CDataInput>(new CNc4DataInput(oss.str(), readComm, multifile, isCollective)); |
---|
626 | else data_in = shared_ptr<CDataInput>(new CNc4DataInput(oss.str(), readComm, multifile, isCollective, time_counter_name)); |
---|
627 | isOpen = true; |
---|
628 | } |
---|
629 | } |
---|
630 | |
---|
631 | //! Close file |
---|
632 | void CFile::close(void) |
---|
633 | { |
---|
634 | if (!allDomainEmpty) |
---|
635 | if (isOpen) |
---|
636 | { |
---|
637 | if (mode.isEmpty() || mode.getValue() == mode_attr::write) |
---|
638 | this->data_out->closeFile(); |
---|
639 | else |
---|
640 | this->data_in->closeFile(); |
---|
641 | } |
---|
642 | if (fileComm != MPI_COMM_NULL) MPI_Comm_free(&fileComm); |
---|
643 | } |
---|
644 | //---------------------------------------------------------------- |
---|
645 | |
---|
646 | void CFile::readAttributesOfEnabledFieldsInReadMode() |
---|
647 | { |
---|
648 | if (enabledFields.empty()) return; |
---|
649 | |
---|
650 | // Just check file and try to open it |
---|
651 | if (time_counter_name.isEmpty()) time_counter_name = "time_counter"; |
---|
652 | |
---|
653 | checkReadFile(); |
---|
654 | |
---|
655 | for (int idx = 0; idx < enabledFields.size(); ++idx) |
---|
656 | { |
---|
657 | // First of all, find out which domain and axis associated with this field |
---|
658 | enabledFields[idx]->solveGridReference(); |
---|
659 | |
---|
660 | // Read attributes of domain and axis from this file |
---|
661 | this->data_in->readFieldAttributesMetaData(enabledFields[idx]); |
---|
662 | |
---|
663 | // Now complete domain and axis associated with this field |
---|
664 | enabledFields[idx]->solveGenerateGrid(); |
---|
665 | |
---|
666 | // Read necessary value from file |
---|
667 | this->data_in->readFieldAttributesValues(enabledFields[idx]); |
---|
668 | |
---|
669 | // Fill attributes for base reference |
---|
670 | enabledFields[idx]->solveGridDomainAxisBaseRef(); |
---|
671 | } |
---|
672 | |
---|
673 | // Now everything is ok, close it |
---|
674 | close(); |
---|
675 | } |
---|
676 | |
---|
677 | |
---|
678 | /*! |
---|
679 | \brief Parse xml file and write information into file object |
---|
680 | \param [in] node xmld node corresponding in xml file |
---|
681 | */ |
---|
682 | void CFile::parse(xml::CXMLNode & node) |
---|
683 | { |
---|
684 | SuperClass::parse(node); |
---|
685 | |
---|
686 | if (node.goToChildElement()) |
---|
687 | { |
---|
688 | do |
---|
689 | { |
---|
690 | if (node.getElementName()=="field" || node.getElementName()=="field_group") this->getVirtualFieldGroup()->parseChild(node); |
---|
691 | else if (node.getElementName()=="variable" || node.getElementName()=="variable_group") this->getVirtualVariableGroup()->parseChild(node); |
---|
692 | } while (node.goToNextElement()); |
---|
693 | node.goToParentElement(); |
---|
694 | } |
---|
695 | |
---|
696 | } |
---|
697 | //---------------------------------------------------------------- |
---|
698 | |
---|
699 | /*! |
---|
700 | \brief Represent a file in form of string with all its info |
---|
701 | \return String |
---|
702 | */ |
---|
703 | StdString CFile::toString(void) const |
---|
704 | { |
---|
705 | StdOStringStream oss; |
---|
706 | |
---|
707 | oss << "<" << CFile::GetName() << " "; |
---|
708 | if (this->hasId()) |
---|
709 | oss << " id=\"" << this->getId() << "\" "; |
---|
710 | oss << SuperClassAttribute::toString() << ">" << std::endl; |
---|
711 | if (this->getVirtualFieldGroup() != NULL) |
---|
712 | oss << *this->getVirtualFieldGroup() << std::endl; |
---|
713 | oss << "</" << CFile::GetName() << " >"; |
---|
714 | return (oss.str()); |
---|
715 | } |
---|
716 | |
---|
717 | //---------------------------------------------------------------- |
---|
718 | |
---|
719 | /*! |
---|
720 | \brief Find all inheritace among objects in a file. |
---|
721 | \param [in] apply (true) write attributes of parent into ones of child if they are empty |
---|
722 | (false) write attributes of parent into a new container of child |
---|
723 | \param [in] parent |
---|
724 | */ |
---|
725 | void CFile::solveDescInheritance(bool apply, const CAttributeMap * const parent) |
---|
726 | { |
---|
727 | SuperClassAttribute::setAttributes(parent,apply); |
---|
728 | this->getVirtualFieldGroup()->solveDescInheritance(apply, NULL); |
---|
729 | this->getVirtualVariableGroup()->solveDescInheritance(apply, NULL); |
---|
730 | } |
---|
731 | |
---|
732 | //---------------------------------------------------------------- |
---|
733 | |
---|
734 | /*! |
---|
735 | \brief Resolve all reference of active fields. |
---|
736 | In order to know exactly which data each active field has, a search for all its |
---|
737 | reference to find its parents or/and its base reference object must be done. Moreover |
---|
738 | during this search, there are some information that can only be sent to server AFTER |
---|
739 | all information of active fields are created on server side, e.g: checking mask or index |
---|
740 | \param [in] sendToServer: Send all info to server (true) or only a part of it (false) |
---|
741 | */ |
---|
742 | void CFile::solveOnlyRefOfEnabledFields(bool sendToServer) |
---|
743 | { |
---|
744 | int size = this->enabledFields.size(); |
---|
745 | for (int i = 0; i < size; ++i) |
---|
746 | { |
---|
747 | this->enabledFields[i]->solveOnlyReferenceEnabledField(sendToServer); |
---|
748 | } |
---|
749 | } |
---|
750 | |
---|
751 | void CFile::checkGridOfEnabledFields() |
---|
752 | { |
---|
753 | int size = this->enabledFields.size(); |
---|
754 | for (int i = 0; i < size; ++i) |
---|
755 | { |
---|
756 | this->enabledFields[i]->checkGridOfEnabledFields(); |
---|
757 | } |
---|
758 | } |
---|
759 | |
---|
760 | void CFile::sendGridOfEnabledFields() |
---|
761 | { |
---|
762 | int size = this->enabledFields.size(); |
---|
763 | for (int i = 0; i < size; ++i) |
---|
764 | { |
---|
765 | this->enabledFields[i]->sendGridOfEnabledFields(); |
---|
766 | } |
---|
767 | } |
---|
768 | |
---|
769 | void CFile::generateNewTransformationGridDest() |
---|
770 | { |
---|
771 | int size = this->enabledFields.size(); |
---|
772 | for (int i = 0; i < size; ++i) |
---|
773 | { |
---|
774 | this->enabledFields[i]->generateNewTransformationGridDest(); |
---|
775 | } |
---|
776 | } |
---|
777 | |
---|
778 | /*! |
---|
779 | \brief Resolve all reference of active fields. |
---|
780 | In order to know exactly which data each active field has, a search for all its |
---|
781 | reference to find its parents or/and its base reference object must be done. Moreover |
---|
782 | during this search, there are some information that can only be sent to server AFTER |
---|
783 | all information of active fields are created on server side, e.g: checking mask or index |
---|
784 | \param [in] sendToServer: Send all info to server (true) or only a part of it (false) |
---|
785 | */ |
---|
786 | void CFile::solveAllRefOfEnabledFieldsAndTransform(bool sendToServer) |
---|
787 | { |
---|
788 | int size = this->enabledFields.size(); |
---|
789 | for (int i = 0; i < size; ++i) |
---|
790 | { |
---|
791 | this->enabledFields[i]->solveAllEnabledFieldsAndTransform(); |
---|
792 | } |
---|
793 | } |
---|
794 | |
---|
795 | /*! |
---|
796 | * Constructs the filter graph for each active field. |
---|
797 | * |
---|
798 | * \param gc the garbage collector to use when building the filter graph |
---|
799 | */ |
---|
800 | void CFile::buildFilterGraphOfEnabledFields(CGarbageCollector& gc) |
---|
801 | { |
---|
802 | int size = this->enabledFields.size(); |
---|
803 | for (int i = 0; i < size; ++i) |
---|
804 | { |
---|
805 | this->enabledFields[i]->buildFilterGraph(gc, true); |
---|
806 | } |
---|
807 | } |
---|
808 | |
---|
809 | /*! |
---|
810 | Prefetching the data for enabled fields read from file. |
---|
811 | */ |
---|
812 | void CFile::prefetchEnabledReadModeFields(void) |
---|
813 | { |
---|
814 | if (mode.isEmpty() || mode.getValue() != mode_attr::read) |
---|
815 | return; |
---|
816 | |
---|
817 | int size = this->enabledFields.size(); |
---|
818 | for (int i = 0; i < size; ++i) |
---|
819 | this->enabledFields[i]->sendReadDataRequest(CContext::getCurrent()->getCalendar()->getCurrentDate()); |
---|
820 | } |
---|
821 | |
---|
822 | /*! |
---|
823 | Prefetching the data for enabled fields read from file whose data is out-of-date. |
---|
824 | */ |
---|
825 | void CFile::prefetchEnabledReadModeFieldsIfNeeded(void) |
---|
826 | { |
---|
827 | if (mode.isEmpty() || mode.getValue() != mode_attr::read) |
---|
828 | return; |
---|
829 | |
---|
830 | int size = this->enabledFields.size(); |
---|
831 | for (int i = 0; i < size; ++i) |
---|
832 | this->enabledFields[i]->sendReadDataRequestIfNeeded(); |
---|
833 | } |
---|
834 | |
---|
835 | void CFile::solveFieldRefInheritance(bool apply) |
---|
836 | { |
---|
837 | // Rsolution des hritages par rfrence de chacun des champs contenus dans le fichier. |
---|
838 | std::vector<CField*> allF = this->getAllFields(); |
---|
839 | for (unsigned int i = 0; i < allF.size(); i++) |
---|
840 | allF[i]->solveRefInheritance(apply); |
---|
841 | } |
---|
842 | |
---|
843 | //---------------------------------------------------------------- |
---|
844 | |
---|
845 | /*! |
---|
846 | \brief Add a field into file. |
---|
847 | A field is added into file and it will be written out if the file is enabled and |
---|
848 | level of this field is smaller than level_output. A new field won't be created if one |
---|
849 | with id has already existed |
---|
850 | \param [in] id String identity of new field |
---|
851 | \return Pointer to added (or already existed) field |
---|
852 | */ |
---|
853 | CField* CFile::addField(const string& id) |
---|
854 | { |
---|
855 | return vFieldGroup->createChild(id); |
---|
856 | } |
---|
857 | |
---|
858 | /*! |
---|
859 | \brief Add a field group into file. |
---|
860 | A field group is added into file and it will play a role as parents for fields. |
---|
861 | A new field group won't be created if one with id has already existed |
---|
862 | \param [in] id String identity of new field group |
---|
863 | \return Pointer to added (or already existed) field group |
---|
864 | */ |
---|
865 | CFieldGroup* CFile::addFieldGroup(const string& id) |
---|
866 | { |
---|
867 | return vFieldGroup->createChildGroup(id); |
---|
868 | } |
---|
869 | |
---|
870 | /*! |
---|
871 | \brief Add a variable into file. |
---|
872 | A variable is added into file and if one with id has already existed, pointer to |
---|
873 | it will be returned. |
---|
874 | Variable as long as attributes are information container of file. |
---|
875 | However, whereas attributes are "fixed" information, variables provides a more flexible way to user |
---|
876 | to fill in (extra) information for a file. |
---|
877 | \param [in] id String identity of new variable |
---|
878 | \return Pointer to added (or already existed) variable |
---|
879 | */ |
---|
880 | CVariable* CFile::addVariable(const string& id) |
---|
881 | { |
---|
882 | return vVariableGroup->createChild(id); |
---|
883 | } |
---|
884 | |
---|
885 | /*! |
---|
886 | \brief Add a variable group into file. |
---|
887 | A variable group is added into file and it will play a role as parents for variables. |
---|
888 | A new variable group won't be created if one with id has already existed |
---|
889 | \param [in] id String identity of new variable group |
---|
890 | \return Pointer to added (or already existed) variable group |
---|
891 | */ |
---|
892 | CVariableGroup* CFile::addVariableGroup(const string& id) |
---|
893 | { |
---|
894 | return vVariableGroup->createChildGroup(id); |
---|
895 | } |
---|
896 | |
---|
897 | void CFile::setContextClient(CContextClient* newContextClient) |
---|
898 | { |
---|
899 | client = newContextClient; |
---|
900 | } |
---|
901 | |
---|
902 | CContextClient* CFile::getContextClient() |
---|
903 | { |
---|
904 | return client; |
---|
905 | } |
---|
906 | |
---|
907 | /*! |
---|
908 | \brief Send a message to create a field on server side |
---|
909 | \param[in] id String identity of field that will be created on server |
---|
910 | */ |
---|
911 | void CFile::sendAddField(const string& id, CContextClient* client) |
---|
912 | { |
---|
913 | sendAddItem(id, EVENT_ID_ADD_FIELD, client); |
---|
914 | } |
---|
915 | |
---|
916 | /*! |
---|
917 | \brief Send a message to create a field group on server side |
---|
918 | \param[in] id String identity of field group that will be created on server |
---|
919 | */ |
---|
920 | void CFile::sendAddFieldGroup(const string& id, CContextClient* client) |
---|
921 | { |
---|
922 | sendAddItem(id, (int)EVENT_ID_ADD_FIELD_GROUP, client); |
---|
923 | } |
---|
924 | |
---|
925 | /*! |
---|
926 | \brief Receive a message annoucing the creation of a field on server side |
---|
927 | \param[in] event Received event |
---|
928 | */ |
---|
929 | void CFile::recvAddField(CEventServer& event) |
---|
930 | { |
---|
931 | |
---|
932 | CBufferIn* buffer = event.subEvents.begin()->buffer; |
---|
933 | string id; |
---|
934 | *buffer>>id; |
---|
935 | get(id)->recvAddField(*buffer); |
---|
936 | } |
---|
937 | |
---|
938 | /*! |
---|
939 | \brief Receive a message annoucing the creation of a field on server side |
---|
940 | \param[in] buffer Buffer containing message |
---|
941 | */ |
---|
942 | void CFile::recvAddField(CBufferIn& buffer) |
---|
943 | { |
---|
944 | string id; |
---|
945 | buffer>>id; |
---|
946 | addField(id); |
---|
947 | } |
---|
948 | |
---|
949 | /*! |
---|
950 | \brief Receive a message annoucing the creation of a field group on server side |
---|
951 | \param[in] event Received event |
---|
952 | */ |
---|
953 | void CFile::recvAddFieldGroup(CEventServer& event) |
---|
954 | { |
---|
955 | |
---|
956 | CBufferIn* buffer = event.subEvents.begin()->buffer; |
---|
957 | string id; |
---|
958 | *buffer>>id; |
---|
959 | get(id)->recvAddFieldGroup(*buffer); |
---|
960 | } |
---|
961 | |
---|
962 | /*! |
---|
963 | \brief Receive a message annoucing the creation of a field group on server side |
---|
964 | \param[in] buffer Buffer containing message |
---|
965 | */ |
---|
966 | void CFile::recvAddFieldGroup(CBufferIn& buffer) |
---|
967 | { |
---|
968 | string id; |
---|
969 | buffer>>id; |
---|
970 | addFieldGroup(id); |
---|
971 | } |
---|
972 | |
---|
973 | /*! |
---|
974 | \brief Send messages to duplicate all variables on server side |
---|
975 | Because each variable has also its attributes. So first thing to do is replicate |
---|
976 | all these attributes on server side. Because variable can have a value, the second thing |
---|
977 | is to duplicate this value on server, too. |
---|
978 | */ |
---|
979 | void CFile::sendAddAllVariables(CContextClient* client) |
---|
980 | { |
---|
981 | std::vector<CVariable*> allVar = getAllVariables(); |
---|
982 | std::vector<CVariable*>::const_iterator it = allVar.begin(); |
---|
983 | std::vector<CVariable*>::const_iterator itE = allVar.end(); |
---|
984 | |
---|
985 | for (; it != itE; ++it) |
---|
986 | { |
---|
987 | this->sendAddVariable((*it)->getId(), client); |
---|
988 | (*it)->sendAllAttributesToServer(client); |
---|
989 | (*it)->sendValue(client); |
---|
990 | } |
---|
991 | } |
---|
992 | |
---|
993 | /*! |
---|
994 | \brief Send a message to create a variable group on server side |
---|
995 | \param[in] id String identity of variable group that will be created on server |
---|
996 | \param [in] client client to which we will send this adding action |
---|
997 | */ |
---|
998 | void CFile::sendAddVariableGroup(const string& id, CContextClient* client) |
---|
999 | { |
---|
1000 | sendAddItem(id, (int)EVENT_ID_ADD_VARIABLE_GROUP, client); |
---|
1001 | } |
---|
1002 | |
---|
1003 | /* |
---|
1004 | Send message to add a variable into a file within a certain client |
---|
1005 | \param [in] id String identity of a variable |
---|
1006 | \param [in] client client to which we will send this adding action |
---|
1007 | */ |
---|
1008 | void CFile::sendAddVariable(const string& id, CContextClient* client) |
---|
1009 | { |
---|
1010 | sendAddItem(id, (int)EVENT_ID_ADD_VARIABLE, client); |
---|
1011 | } |
---|
1012 | |
---|
1013 | /*! |
---|
1014 | \brief Receive a message annoucing the creation of a variable on server side |
---|
1015 | \param[in] event Received event |
---|
1016 | */ |
---|
1017 | void CFile::recvAddVariable(CEventServer& event) |
---|
1018 | { |
---|
1019 | |
---|
1020 | CBufferIn* buffer = event.subEvents.begin()->buffer; |
---|
1021 | string id; |
---|
1022 | *buffer>>id; |
---|
1023 | get(id)->recvAddVariable(*buffer); |
---|
1024 | } |
---|
1025 | |
---|
1026 | /*! |
---|
1027 | \brief Receive a message annoucing the creation of a variable on server side |
---|
1028 | \param[in] buffer Buffer containing message |
---|
1029 | */ |
---|
1030 | void CFile::recvAddVariable(CBufferIn& buffer) |
---|
1031 | { |
---|
1032 | string id; |
---|
1033 | buffer>>id; |
---|
1034 | addVariable(id); |
---|
1035 | } |
---|
1036 | |
---|
1037 | /*! |
---|
1038 | \brief Receive a message annoucing the creation of a variable group on server side |
---|
1039 | \param[in] event Received event |
---|
1040 | */ |
---|
1041 | void CFile::recvAddVariableGroup(CEventServer& event) |
---|
1042 | { |
---|
1043 | |
---|
1044 | CBufferIn* buffer = event.subEvents.begin()->buffer; |
---|
1045 | string id; |
---|
1046 | *buffer>>id; |
---|
1047 | get(id)->recvAddVariableGroup(*buffer); |
---|
1048 | } |
---|
1049 | |
---|
1050 | /*! |
---|
1051 | \brief Receive a message annoucing the creation of a variable group on server side |
---|
1052 | \param[in] buffer Buffer containing message |
---|
1053 | */ |
---|
1054 | void CFile::recvAddVariableGroup(CBufferIn& buffer) |
---|
1055 | { |
---|
1056 | string id; |
---|
1057 | buffer>>id; |
---|
1058 | addVariableGroup(id); |
---|
1059 | } |
---|
1060 | |
---|
1061 | /*! |
---|
1062 | \brief Sending all active (enabled) fields from client to server. |
---|
1063 | Each field is identified uniquely by its string identity. Not only should we |
---|
1064 | send the id to server but also we need to send ids of reference domain and reference axis. |
---|
1065 | With these two id, it's easier to make reference to grid where all data should be written. |
---|
1066 | Remark: This function must be called AFTER all active (enabled) files have been created on the server side |
---|
1067 | */ |
---|
1068 | void CFile::sendEnabledFields(CContextClient* client) |
---|
1069 | { |
---|
1070 | size_t size = this->enabledFields.size(); |
---|
1071 | for (size_t i = 0; i < size; ++i) |
---|
1072 | { |
---|
1073 | CField* field = this->enabledFields[i]; |
---|
1074 | this->sendAddField(field->getId(), client); |
---|
1075 | field->sendAllAttributesToServer(client); |
---|
1076 | field->sendAddAllVariables(client); |
---|
1077 | } |
---|
1078 | } |
---|
1079 | |
---|
1080 | |
---|
1081 | /*! |
---|
1082 | \brief Dispatch event received from client |
---|
1083 | Whenever a message is received in buffer of server, it will be processed depending on |
---|
1084 | its event type. A new event type should be added in the switch list to make sure |
---|
1085 | it processed on server side. |
---|
1086 | \param [in] event: Received message |
---|
1087 | */ |
---|
1088 | bool CFile::dispatchEvent(CEventServer& event) |
---|
1089 | { |
---|
1090 | if (SuperClass::dispatchEvent(event)) return true; |
---|
1091 | else |
---|
1092 | { |
---|
1093 | switch(event.type) |
---|
1094 | { |
---|
1095 | case EVENT_ID_ADD_FIELD : |
---|
1096 | recvAddField(event); |
---|
1097 | return true; |
---|
1098 | break; |
---|
1099 | |
---|
1100 | case EVENT_ID_ADD_FIELD_GROUP : |
---|
1101 | recvAddFieldGroup(event); |
---|
1102 | return true; |
---|
1103 | break; |
---|
1104 | |
---|
1105 | case EVENT_ID_ADD_VARIABLE : |
---|
1106 | recvAddVariable(event); |
---|
1107 | return true; |
---|
1108 | break; |
---|
1109 | |
---|
1110 | case EVENT_ID_ADD_VARIABLE_GROUP : |
---|
1111 | recvAddVariableGroup(event); |
---|
1112 | return true; |
---|
1113 | break; |
---|
1114 | default : |
---|
1115 | ERROR("bool CFile::dispatchEvent(CEventServer& event)", << "Unknown Event"); |
---|
1116 | return false; |
---|
1117 | } |
---|
1118 | } |
---|
1119 | } |
---|
1120 | |
---|
1121 | |
---|
1122 | |
---|
1123 | |
---|
1124 | ///--------------------------------------------------------------- |
---|
1125 | |
---|
1126 | } // namespace xios |
---|