[528] | 1 | #include <fstream> |
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| 2 | |
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[219] | 3 | #include "onetcdf4.hpp" |
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[352] | 4 | #include "group_template.hpp" |
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[382] | 5 | #include "mpi.hpp" |
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[379] | 6 | #include "netcdf.hpp" |
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[498] | 7 | #include "netCdfInterface.hpp" |
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| 8 | #include "netCdfException.hpp" |
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[1158] | 9 | #include "timer.hpp" |
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[219] | 10 | |
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[335] | 11 | namespace xios |
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[219] | 12 | { |
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| 13 | /// ////////////////////// Définitions ////////////////////// /// |
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| 14 | |
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[686] | 15 | CONetCDF4::CONetCDF4(const StdString& filename, bool append, bool useClassicFormat, |
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[878] | 16 | bool useCFConvention, |
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[1639] | 17 | const MPI_Comm* comm, bool multifile, const StdString& timeCounterName) |
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[686] | 18 | : path() |
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| 19 | , wmpi(false) |
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| 20 | , useClassicFormat(useClassicFormat) |
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[878] | 21 | , useCFConvention(useCFConvention) |
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[219] | 22 | { |
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[878] | 23 | this->initialize(filename, append, useClassicFormat, useCFConvention, comm, multifile, timeCounterName); |
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[219] | 24 | } |
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[498] | 25 | |
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[219] | 26 | //--------------------------------------------------------------- |
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[286] | 27 | |
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[219] | 28 | CONetCDF4::~CONetCDF4(void) |
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| 29 | { |
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| 30 | } |
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| 31 | |
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| 32 | ///-------------------------------------------------------------- |
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| 33 | |
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[878] | 34 | void CONetCDF4::initialize(const StdString& filename, bool append, bool useClassicFormat, bool useCFConvention, |
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[1639] | 35 | const MPI_Comm* comm, bool multifile, const StdString& timeCounterName) |
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[219] | 36 | { |
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[517] | 37 | this->useClassicFormat = useClassicFormat; |
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[878] | 38 | this->useCFConvention = useCFConvention; |
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[517] | 39 | |
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| 40 | int mode = useClassicFormat ? 0 : NC_NETCDF4; |
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[605] | 41 | |
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| 42 | // Don't use parallel mode if there is only one process |
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| 43 | if (comm) |
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| 44 | { |
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| 45 | int commSize = 0; |
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[1639] | 46 | MPI_Comm_size(*comm, &commSize); |
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[605] | 47 | if (commSize <= 1) |
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| 48 | comm = NULL; |
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| 49 | } |
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| 50 | wmpi = comm && !multifile; |
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| 51 | |
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| 52 | if (wmpi) |
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[517] | 53 | mode |= useClassicFormat ? NC_PNETCDF : NC_MPIIO; |
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| 54 | |
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[528] | 55 | // If the file does not exist, we always create it |
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| 56 | if (!append || !std::ifstream(filename.c_str())) |
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[219] | 57 | { |
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[1158] | 58 | CTimer::get("Files : create").resume(); |
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[605] | 59 | if (wmpi) |
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[1639] | 60 | CNetCdfInterface::createPar(filename, mode, *comm, MPI_INFO_NULL, this->ncidp); |
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[605] | 61 | else |
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| 62 | CNetCdfInterface::create(filename, mode, this->ncidp); |
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[1158] | 63 | CTimer::get("Files : create").suspend(); |
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| 64 | |
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[528] | 65 | this->appendMode = false; |
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[219] | 66 | } |
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| 67 | else |
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| 68 | { |
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[528] | 69 | mode |= NC_WRITE; |
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[1158] | 70 | CTimer::get("Files : open").resume(); |
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[605] | 71 | if (wmpi) |
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[1639] | 72 | CNetCdfInterface::openPar(filename, mode, *comm, MPI_INFO_NULL, this->ncidp); |
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[605] | 73 | else |
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| 74 | CNetCdfInterface::open(filename, mode, this->ncidp); |
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[1158] | 75 | CTimer::get("Files : open").suspend(); |
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[528] | 76 | this->appendMode = true; |
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[219] | 77 | } |
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[517] | 78 | |
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| 79 | // If the classic NetCDF format is used, we enable the "no-fill mode" globally. |
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| 80 | // This is done per variable for the NetCDF4 format. |
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| 81 | if (useClassicFormat) |
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[606] | 82 | CNetCdfInterface::setFill(this->ncidp, false); |
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[802] | 83 | |
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| 84 | this->timeCounterName = timeCounterName; |
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[219] | 85 | } |
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[498] | 86 | |
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[286] | 87 | void CONetCDF4::close() |
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| 88 | { |
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[1158] | 89 | CTimer::get("Files : close").resume(); |
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[686] | 90 | CNetCdfInterface::close(this->ncidp); |
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[1158] | 91 | CTimer::get("Files : close").suspend(); |
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[286] | 92 | } |
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[498] | 93 | |
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[219] | 94 | //--------------------------------------------------------------- |
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[498] | 95 | |
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[219] | 96 | void CONetCDF4::definition_start(void) |
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[498] | 97 | { |
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[686] | 98 | CNetCdfInterface::reDef(this->ncidp); |
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[219] | 99 | } |
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[498] | 100 | |
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[219] | 101 | //--------------------------------------------------------------- |
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[498] | 102 | |
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[219] | 103 | void CONetCDF4::definition_end(void) |
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| 104 | { |
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[686] | 105 | CNetCdfInterface::endDef(this->ncidp); |
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[219] | 106 | } |
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| 107 | |
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| 108 | //--------------------------------------------------------------- |
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[498] | 109 | |
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[219] | 110 | int CONetCDF4::getCurrentGroup(void) |
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| 111 | { |
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[686] | 112 | return this->getGroup(this->getCurrentPath()); |
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[219] | 113 | } |
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[498] | 114 | |
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[219] | 115 | //--------------------------------------------------------------- |
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[498] | 116 | |
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[686] | 117 | int CONetCDF4::getGroup(const CONetCDF4Path& path) |
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[219] | 118 | { |
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| 119 | int retvalue = this->ncidp; |
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[498] | 120 | |
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[686] | 121 | CONetCDF4Path::const_iterator it = path.begin(), end = path.end(); |
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[219] | 122 | |
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[686] | 123 | for (; it != end; it++) |
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[219] | 124 | { |
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[686] | 125 | const StdString& groupid = *it; |
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| 126 | CNetCdfInterface::inqNcId(retvalue, groupid, retvalue); |
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[219] | 127 | } |
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[686] | 128 | return retvalue; |
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[219] | 129 | } |
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[498] | 130 | |
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[219] | 131 | //--------------------------------------------------------------- |
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[498] | 132 | |
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[686] | 133 | int CONetCDF4::getVariable(const StdString& varname) |
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[219] | 134 | { |
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| 135 | int varid = 0; |
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| 136 | int grpid = this->getCurrentGroup(); |
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[686] | 137 | CNetCdfInterface::inqVarId(grpid, varname, varid); |
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| 138 | return varid; |
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[219] | 139 | } |
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[498] | 140 | |
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[219] | 141 | //--------------------------------------------------------------- |
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[498] | 142 | |
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[686] | 143 | int CONetCDF4::getDimension(const StdString& dimname) |
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[219] | 144 | { |
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| 145 | int dimid = 0; |
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| 146 | int grpid = this->getCurrentGroup(); |
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[686] | 147 | CNetCdfInterface::inqDimId(grpid, dimname, dimid); |
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| 148 | return dimid; |
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[219] | 149 | } |
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[498] | 150 | |
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[219] | 151 | //--------------------------------------------------------------- |
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[498] | 152 | |
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[219] | 153 | int CONetCDF4::getUnlimitedDimension(void) |
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| 154 | { |
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| 155 | int dimid = 0; |
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| 156 | int grpid = this->getCurrentGroup(); |
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[686] | 157 | CNetCdfInterface::inqUnLimDim(grpid, dimid); |
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| 158 | return dimid; |
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[219] | 159 | } |
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[498] | 160 | |
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[266] | 161 | StdString CONetCDF4::getUnlimitedDimensionName(void) |
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| 162 | { |
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| 163 | int grpid = this->getGroup(path); |
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| 164 | int dimid = this->getUnlimitedDimension(); |
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[498] | 165 | |
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| 166 | StdString dimname; |
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[686] | 167 | if (dimid != -1) |
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| 168 | CNetCdfInterface::inqDimName(grpid, dimid, dimname); |
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| 169 | return dimname; |
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[266] | 170 | } |
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[498] | 171 | |
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[219] | 172 | //--------------------------------------------------------------- |
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[498] | 173 | |
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[686] | 174 | std::vector<StdSize> CONetCDF4::getDimensions(const StdString& varname) |
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[219] | 175 | { |
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| 176 | StdSize size = 0; |
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| 177 | std::vector<StdSize> retvalue; |
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| 178 | int grpid = this->getCurrentGroup(); |
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| 179 | int varid = this->getVariable(varname); |
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| 180 | int nbdim = 0, *dimid = NULL; |
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| 181 | |
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[686] | 182 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
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[219] | 183 | dimid = new int[nbdim](); |
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[686] | 184 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
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[219] | 185 | |
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| 186 | for (int i = 0; i < nbdim; i++) |
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| 187 | { |
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[686] | 188 | CNetCdfInterface::inqDimLen(grpid, dimid[i], size); |
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[219] | 189 | if (size == NC_UNLIMITED) |
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| 190 | size = UNLIMITED_DIM; |
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| 191 | retvalue.push_back(size); |
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| 192 | } |
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[401] | 193 | delete [] dimid; |
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[686] | 194 | return retvalue; |
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[219] | 195 | } |
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| 196 | |
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[686] | 197 | std::vector<std::string> CONetCDF4::getDimensionsIdList(const std::string* _varname) |
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[266] | 198 | { |
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[498] | 199 | int nDimNull = 0; |
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[266] | 200 | int nbdim = 0, *dimid = NULL; |
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| 201 | int grpid = this->getCurrentGroup(); |
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| 202 | int varid = (_varname != NULL) ? this->getVariable(*_varname) : NC_GLOBAL; |
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| 203 | std::vector<std::string> retvalue; |
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[498] | 204 | |
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[266] | 205 | if (_varname != NULL) |
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| 206 | { |
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[686] | 207 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
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[266] | 208 | dimid = new int[nbdim](); |
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[686] | 209 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
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[266] | 210 | } |
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| 211 | else |
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| 212 | { |
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[686] | 213 | CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1); |
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[266] | 214 | dimid = new int[nbdim](); |
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[686] | 215 | CNetCdfInterface::inqDimIds(grpid, nDimNull, dimid, 1); |
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[266] | 216 | } |
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[498] | 217 | |
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[266] | 218 | for (int i = 0; i < nbdim; i++) |
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| 219 | { |
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[498] | 220 | std::string dimname; |
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[686] | 221 | CNetCdfInterface::inqDimName(grpid, dimid[i], dimname); |
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[266] | 222 | retvalue.push_back(dimname); |
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| 223 | } |
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| 224 | delete [] dimid; |
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[498] | 225 | |
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[686] | 226 | return retvalue; |
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[266] | 227 | } |
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| 228 | |
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[219] | 229 | //--------------------------------------------------------------- |
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| 230 | |
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[707] | 231 | void CONetCDF4::getTimeAxisBounds(CArray<double,2>& timeAxisBounds, const StdString& name, bool collective) |
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| 232 | { |
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| 233 | int grpid = this->getCurrentGroup(); |
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| 234 | int varid = this->getVariable(name); |
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| 235 | |
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| 236 | std::vector<StdSize> start(2), count(2); |
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| 237 | start[0] = 0; |
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| 238 | // Find out how many temporal records have been written already to the file we are opening |
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| 239 | int ncUnlimitedDimId; |
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| 240 | CNetCdfInterface::inqUnLimDim(this->ncidp, ncUnlimitedDimId); |
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| 241 | CNetCdfInterface::inqDimLen(this->ncidp, ncUnlimitedDimId, count[0]); |
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| 242 | start[1] = 0; |
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| 243 | count[1] = 2; |
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| 244 | |
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| 245 | timeAxisBounds.resize(count[1], count[0]); |
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| 246 | |
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| 247 | if (this->wmpi && collective) |
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| 248 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
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| 249 | if (this->wmpi && !collective) |
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| 250 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
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| 251 | |
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| 252 | CNetCdfInterface::getVaraType(grpid, varid, &start[0], &count[0], timeAxisBounds.dataFirst()); |
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| 253 | } |
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| 254 | |
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[1158] | 255 | void CONetCDF4::getTimeAxisBounds(CArray<double,2>& timeAxisBounds, const StdString& name, bool collective, size_t record) |
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| 256 | { |
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| 257 | int grpid = this->getCurrentGroup(); |
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| 258 | int varid = this->getVariable(name); |
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[707] | 259 | |
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[1158] | 260 | std::vector<StdSize> start(2), count(2); |
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| 261 | start[0] = record; |
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| 262 | count[0] = 1 ; |
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| 263 | start[1] = 0; |
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| 264 | count[1] = 2; |
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| 265 | |
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| 266 | timeAxisBounds.resize(2, 1); |
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| 267 | |
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| 268 | if (this->wmpi && collective) |
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| 269 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
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| 270 | if (this->wmpi && !collective) |
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| 271 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
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| 272 | |
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| 273 | CNetCdfInterface::getVaraType(grpid, varid, &start[0], &count[0], timeAxisBounds.dataFirst()); |
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| 274 | } |
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| 275 | |
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| 276 | |
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| 277 | |
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[686] | 278 | const CONetCDF4::CONetCDF4Path& CONetCDF4::getCurrentPath(void) const |
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| 279 | { return this->path; } |
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[219] | 280 | |
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[686] | 281 | void CONetCDF4::setCurrentPath(const CONetCDF4Path& path) |
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[219] | 282 | { this->path = path; } |
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| 283 | |
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| 284 | //--------------------------------------------------------------- |
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| 285 | |
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[686] | 286 | int CONetCDF4::addGroup(const StdString& name) |
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[219] | 287 | { |
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| 288 | int retvalue = 0; |
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| 289 | int grpid = this->getCurrentGroup(); |
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[686] | 290 | CNetCdfInterface::defGrp(grpid, name, retvalue); |
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| 291 | return retvalue; |
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[219] | 292 | } |
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[498] | 293 | |
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[219] | 294 | //--------------------------------------------------------------- |
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[498] | 295 | |
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[219] | 296 | int CONetCDF4::addDimension(const StdString& name, const StdSize size) |
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| 297 | { |
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| 298 | int retvalue = 0; |
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| 299 | int grpid = this->getCurrentGroup(); |
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| 300 | if (size != UNLIMITED_DIM) |
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[686] | 301 | CNetCdfInterface::defDim(grpid, name, size, retvalue); |
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[219] | 302 | else |
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[686] | 303 | CNetCdfInterface::defDim(grpid, name, NC_UNLIMITED, retvalue); |
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| 304 | return retvalue; |
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[219] | 305 | } |
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[498] | 306 | |
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[219] | 307 | //--------------------------------------------------------------- |
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[498] | 308 | |
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[686] | 309 | int CONetCDF4::addVariable(const StdString& name, nc_type type, |
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[2481] | 310 | const std::vector<StdString>& dim, bool defineChunking) |
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[219] | 311 | { |
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[350] | 312 | int varid = 0; |
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[219] | 313 | std::vector<int> dimids; |
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[606] | 314 | std::vector<StdSize> dimsizes; |
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[857] | 315 | int dimSize = dim.size(); |
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[2479] | 316 | |
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[2481] | 317 | StdSize size; |
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| 318 | |
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[2479] | 319 | int grpid = this->getCurrentGroup(); |
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| 320 | |
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| 321 | std::vector<StdString>::const_iterator it = dim.begin(), end = dim.end(); |
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| 322 | |
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| 323 | for (int idx = 0; it != end; it++, ++idx) |
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| 324 | { |
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| 325 | const StdString& dimid = *it; |
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| 326 | dimids.push_back(this->getDimension(dimid)); |
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[2481] | 327 | CNetCdfInterface::inqDimLen(grpid, this->getDimension(dimid), size); |
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| 328 | if (size == NC_UNLIMITED) size = 1; |
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| 329 | dimsizes.push_back(size); |
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[2479] | 330 | } |
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| 331 | |
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| 332 | CNetCdfInterface::defVar(grpid, name, type, dimids.size(), &dimids[0], varid); |
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[2481] | 333 | |
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| 334 | if (defineChunking) { |
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| 335 | int storageType = (0 == dimSize) ? NC_CONTIGUOUS : NC_CHUNKED; |
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| 336 | CNetCdfInterface::defVarChunking(grpid, varid, storageType, &dimsizes[0]); |
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| 337 | CNetCdfInterface::defVarFill(grpid, varid, true, NULL); |
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| 338 | } |
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| 339 | |
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[878] | 340 | |
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[2479] | 341 | return varid; |
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| 342 | } |
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| 343 | |
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| 344 | //--------------------------------------------------------------- |
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| 345 | |
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| 346 | int CONetCDF4::addChunk(CField* field, nc_type type, |
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| 347 | const std::vector<StdString>& dim, int compressionLevel) |
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| 348 | { |
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| 349 | const StdString& name = field->getFieldOutputName(); |
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| 350 | int varid = 0; |
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| 351 | std::vector<StdSize> dimsizes; |
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| 352 | int dimSize = dim.size(); |
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| 353 | |
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[606] | 354 | StdSize size; |
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| 355 | StdSize totalSize; |
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[498] | 356 | |
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[2479] | 357 | // default chunk size |
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| 358 | StdSize maxSize = 1024 * 1024 * 20; // = 20 Mo (exp using large NEMO like grids) |
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| 359 | StdSize targetSize = maxSize; |
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| 360 | if (!field->chunking_blocksize_target.isEmpty()) |
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| 361 | { |
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| 362 | targetSize = field->chunking_blocksize_target.getValue()*1024*1024; |
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| 363 | } |
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| 364 | StdSize recordSize = 1; //sizeof(type); |
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| 365 | if (field->prec.isEmpty()) recordSize *= 4; |
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| 366 | else recordSize *= field->prec; |
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| 367 | |
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[219] | 368 | int grpid = this->getCurrentGroup(); |
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[498] | 369 | |
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[606] | 370 | std::vector<StdString>::const_iterator it = dim.begin(), end = dim.end(); |
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[219] | 371 | |
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[878] | 372 | for (int idx = 0; it != end; it++, ++idx) |
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[219] | 373 | { |
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[686] | 374 | const StdString& dimid = *it; |
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[606] | 375 | CNetCdfInterface::inqDimLen(grpid, this->getDimension(dimid), size); |
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| 376 | if (size == NC_UNLIMITED) size = 1; |
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[2479] | 377 | recordSize *= size; |
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[606] | 378 | dimsizes.push_back(size); |
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[219] | 379 | } |
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[2479] | 380 | double chunkingRatio = (double)recordSize / (double)targetSize; |
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[453] | 381 | |
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[2479] | 382 | varid = this->getVariable(name); |
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[498] | 383 | |
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[517] | 384 | // The classic NetCDF format does not support chunking nor fill parameters |
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| 385 | if (!useClassicFormat) |
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[453] | 386 | { |
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[2479] | 387 | // Browse field's elements (domain, axis) and NetCDF meta-data to retrieve corresponding chunking coefficients |
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| 388 | // in the file order ! |
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| 389 | CGrid* grid = field->getGrid(); |
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| 390 | std::vector<CDomain*> domains = grid->getDomains(); |
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| 391 | std::vector<CAxis*> axis = grid->getAxis(); |
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| 392 | |
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| 393 | std::vector<double> userChunkingWeights; // store chunking coefficients defined by users |
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| 394 | std::vector<StdString>::const_reverse_iterator itId = dim.rbegin(); // NetCDF is fed using dim, see this::addVariable() |
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| 395 | int elementIdx(0); |
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| 396 | int outerAxis(-1), outerDomJ(-1), outerDomI(-1); |
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| 397 | for (vector<StdSize>::reverse_iterator itDim = dimsizes.rbegin(); itDim != dimsizes.rend(); ++itDim, ++itId, ++elementIdx) |
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[517] | 398 | { |
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[2479] | 399 | bool isAxis(false); |
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| 400 | for ( auto ax : axis ) |
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| 401 | { |
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| 402 | StdString axisDim; |
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| 403 | // Rebuild axis name from axis before comparing |
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| 404 | if (ax->dim_name.isEmpty()) axisDim = ax->getAxisOutputName(); |
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| 405 | else axisDim=ax->dim_name.getValue(); |
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| 406 | if (axisDim == *itId) |
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| 407 | { |
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| 408 | if (!ax->chunking_weight.isEmpty()) userChunkingWeights.push_back( ax->chunking_weight.getValue() ); |
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| 409 | else userChunkingWeights.push_back( 0. ); |
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| 410 | isAxis = true; |
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| 411 | outerAxis = elementIdx; // Going backward in dimsizes, overwriting will keep outer |
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| 412 | break; |
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| 413 | } |
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| 414 | } // end scanning axis |
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| 415 | bool isDomain(false); |
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| 416 | for ( auto dom : domains ) |
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| 417 | { |
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| 418 | StdString axisDim; |
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| 419 | // Rebuild axis I name from domain before comparing |
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| 420 | if (!dom->dim_i_name.isEmpty()) axisDim = dom->dim_i_name.getValue(); |
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| 421 | else |
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| 422 | { |
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| 423 | if (dom->type==CDomain::type_attr::curvilinear) axisDim="x"; |
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| 424 | if (dom->type==CDomain::type_attr::unstructured) axisDim="cell"; |
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| 425 | if (dom->type==CDomain::type_attr::rectilinear) axisDim="lon"; |
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| 426 | } |
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| 427 | if (axisDim == *itId) |
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| 428 | { |
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| 429 | if (!dom->chunking_weight_i.isEmpty()) userChunkingWeights.push_back( dom->chunking_weight_i.getValue() ); |
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| 430 | else userChunkingWeights.push_back( 0. ); |
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| 431 | isDomain = true; |
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| 432 | outerDomI = elementIdx; // Going backward in dimsizes, overwriting will keep outer |
---|
| 433 | break; |
---|
| 434 | } |
---|
| 435 | // Rebuild axis J name from domain before comparing |
---|
| 436 | if (!dom->dim_j_name.isEmpty()) axisDim = dom->dim_j_name.getValue(); |
---|
| 437 | else { |
---|
| 438 | if (dom->type==CDomain::type_attr::curvilinear) axisDim="y"; |
---|
| 439 | if (dom->type==CDomain::type_attr::rectilinear) axisDim="lat"; |
---|
| 440 | } |
---|
| 441 | if (axisDim == *itId) |
---|
| 442 | { |
---|
| 443 | if (!dom->chunking_weight_j.isEmpty()) userChunkingWeights.push_back( dom->chunking_weight_j.getValue() ); |
---|
| 444 | else userChunkingWeights.push_back( 0. ); |
---|
| 445 | outerDomJ = elementIdx; // Going backward in dimsizes, overwriting will keep outer |
---|
| 446 | isDomain = true; |
---|
| 447 | break; |
---|
| 448 | } |
---|
| 449 | } // end scanning domain |
---|
| 450 | // No chunking applied on scalars or time |
---|
| 451 | if ((!isAxis)&&(!isDomain)) |
---|
| 452 | { |
---|
| 453 | userChunkingWeights.push_back( 0. ); |
---|
| 454 | } |
---|
[517] | 455 | } |
---|
[2479] | 456 | |
---|
| 457 | double sumChunkingWeights(0); |
---|
| 458 | for (int i=0;i<userChunkingWeights.size();i++) sumChunkingWeights += userChunkingWeights[i]; |
---|
| 459 | if ( (!sumChunkingWeights) && (chunkingRatio > 1) ) |
---|
| 460 | { |
---|
| 461 | if (outerAxis!=-1) userChunkingWeights[outerAxis] = 1; // chunk along outer axis |
---|
| 462 | else if (outerDomJ!=-1) userChunkingWeights[outerDomJ] = 1; // if no axis ? -> along j |
---|
| 463 | else if (outerDomI!=-1) userChunkingWeights[outerDomI] = 1; // if no j -> along i |
---|
| 464 | else {;} |
---|
| 465 | } |
---|
| 466 | |
---|
| 467 | int countChunkingDims(0); // number of dimensions on which chunking is operated : algo uses pow(value, 1/countChunkingDims) |
---|
| 468 | double normalizingWeight(0); // use to relativize chunking coefficients for all dimensions |
---|
| 469 | for (int i=0;i<userChunkingWeights.size();i++) |
---|
| 470 | if (userChunkingWeights[i]>0.) |
---|
| 471 | { |
---|
| 472 | countChunkingDims++; |
---|
| 473 | normalizingWeight = userChunkingWeights[i]; |
---|
| 474 | } |
---|
| 475 | |
---|
| 476 | std::vector<double> chunkingRatioPerDims; // will store coefficients used to compute chunk size |
---|
| 477 | double productRatios = 1; // last_coeff = pow( shrink_ratio / (product of all ratios), 1/countChunkingDims ) |
---|
| 478 | for (int i=0;i<userChunkingWeights.size();i++) |
---|
| 479 | { |
---|
| 480 | chunkingRatioPerDims.push_back( userChunkingWeights[i] / normalizingWeight ); |
---|
| 481 | if (chunkingRatioPerDims[i]) productRatios *= chunkingRatioPerDims[i]; |
---|
| 482 | } |
---|
| 483 | for (int i=0;i<userChunkingWeights.size();i++) |
---|
| 484 | { |
---|
| 485 | chunkingRatioPerDims[i] *= pow( chunkingRatio / productRatios, 1./countChunkingDims ); |
---|
| 486 | } |
---|
| 487 | |
---|
| 488 | std::vector<double>::iterator itChunkingRatios = chunkingRatioPerDims.begin(); |
---|
| 489 | //itId = dim.rbegin(); |
---|
| 490 | double correctionFromPreviousDim = 1.; |
---|
| 491 | for (vector<StdSize>::reverse_iterator itDim = dimsizes.rbegin(); itDim != dimsizes.rend(); ++itDim, ++itChunkingRatios, ++itId) |
---|
| 492 | { |
---|
| 493 | *itChunkingRatios *= correctionFromPreviousDim; |
---|
| 494 | correctionFromPreviousDim = 1; |
---|
| 495 | if (*itChunkingRatios > 1) // else target larger than size ! |
---|
| 496 | { |
---|
| 497 | StdSize dimensionSize = *itDim; |
---|
| 498 | //info(0) << *itId << " " << *itDim << " " << *itChunkingRatios << " " << (*itDim)/(*itChunkingRatios) << endl; |
---|
| 499 | *itDim = ceil( *itDim / ceil(*itChunkingRatios) ); |
---|
| 500 | correctionFromPreviousDim = *itChunkingRatios/ ((double)dimensionSize/(*itDim)); |
---|
| 501 | } |
---|
| 502 | } |
---|
[857] | 503 | int storageType = (0 == dimSize) ? NC_CONTIGUOUS : NC_CHUNKED; |
---|
| 504 | CNetCdfInterface::defVarChunking(grpid, varid, storageType, &dimsizes[0]); |
---|
[517] | 505 | CNetCdfInterface::defVarFill(grpid, varid, true, NULL); |
---|
[453] | 506 | } |
---|
| 507 | |
---|
[1456] | 508 | setCompressionLevel(name, compressionLevel) ; |
---|
| 509 | |
---|
[606] | 510 | return varid; |
---|
[219] | 511 | } |
---|
| 512 | |
---|
| 513 | //--------------------------------------------------------------- |
---|
| 514 | |
---|
[606] | 515 | void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel) |
---|
| 516 | { |
---|
[607] | 517 | if (compressionLevel < 0 || compressionLevel > 9) |
---|
| 518 | ERROR("void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel)", |
---|
| 519 | "Invalid compression level for variable \"" << varname << "\", the value should range between 0 and 9."); |
---|
| 520 | if (compressionLevel && wmpi) |
---|
| 521 | ERROR("void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel)", |
---|
| 522 | "Impossible to use compression for variable \"" << varname << "\" when using parallel mode."); |
---|
[606] | 523 | int grpid = this->getCurrentGroup(); |
---|
| 524 | int varid = this->getVariable(varname); |
---|
| 525 | CNetCdfInterface::defVarDeflate(grpid, varid, compressionLevel); |
---|
| 526 | } |
---|
| 527 | |
---|
| 528 | //--------------------------------------------------------------- |
---|
| 529 | |
---|
[219] | 530 | template <> |
---|
[686] | 531 | void CONetCDF4::addAttribute(const StdString& name, const StdString& value, const StdString* varname) |
---|
[219] | 532 | { |
---|
| 533 | int grpid = this->getCurrentGroup(); |
---|
| 534 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 535 | CNetCdfInterface::putAttType(grpid, varid, name, value.size(), value.c_str()); |
---|
[219] | 536 | } |
---|
[498] | 537 | |
---|
[219] | 538 | //--------------------------------------------------------------- |
---|
[498] | 539 | |
---|
[219] | 540 | template <> |
---|
[686] | 541 | void CONetCDF4::addAttribute(const StdString& name, const double& value, const StdString* varname) |
---|
[219] | 542 | { |
---|
| 543 | int grpid = this->getCurrentGroup(); |
---|
| 544 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 545 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[219] | 546 | } |
---|
[391] | 547 | |
---|
[686] | 548 | template <> |
---|
| 549 | void CONetCDF4::addAttribute(const StdString& name, const CArray<double,1>& value, const StdString* varname) |
---|
[391] | 550 | { |
---|
| 551 | int grpid = this->getCurrentGroup(); |
---|
| 552 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 553 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 554 | } |
---|
[219] | 555 | //--------------------------------------------------------------- |
---|
[498] | 556 | |
---|
[219] | 557 | template <> |
---|
[686] | 558 | void CONetCDF4::addAttribute(const StdString& name, const float& value, const StdString* varname) |
---|
[219] | 559 | { |
---|
| 560 | int grpid = this->getCurrentGroup(); |
---|
| 561 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 562 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[219] | 563 | } |
---|
[391] | 564 | |
---|
[686] | 565 | template <> |
---|
| 566 | void CONetCDF4::addAttribute(const StdString& name, const CArray<float,1>& value, const StdString* varname) |
---|
[391] | 567 | { |
---|
| 568 | int grpid = this->getCurrentGroup(); |
---|
| 569 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 570 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 571 | } |
---|
| 572 | |
---|
[219] | 573 | //--------------------------------------------------------------- |
---|
[498] | 574 | |
---|
[219] | 575 | template <> |
---|
[686] | 576 | void CONetCDF4::addAttribute(const StdString& name, const int& value, const StdString* varname) |
---|
[219] | 577 | { |
---|
| 578 | int grpid = this->getCurrentGroup(); |
---|
| 579 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 580 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[219] | 581 | } |
---|
| 582 | |
---|
[686] | 583 | template <> |
---|
| 584 | void CONetCDF4::addAttribute(const StdString& name, const CArray<int,1>& value, const StdString* varname) |
---|
[391] | 585 | { |
---|
| 586 | int grpid = this->getCurrentGroup(); |
---|
| 587 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 588 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 589 | } |
---|
| 590 | |
---|
[472] | 591 | template <> |
---|
[686] | 592 | void CONetCDF4::addAttribute(const StdString& name, const short int& value, const StdString* varname) |
---|
[472] | 593 | { |
---|
| 594 | int grpid = this->getCurrentGroup(); |
---|
| 595 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 596 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[472] | 597 | } |
---|
[219] | 598 | |
---|
[686] | 599 | template <> |
---|
| 600 | void CONetCDF4::addAttribute(const StdString& name, const CArray<short int,1>& value, const StdString* varname) |
---|
[472] | 601 | { |
---|
| 602 | int grpid = this->getCurrentGroup(); |
---|
| 603 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 604 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 605 | } |
---|
| 606 | |
---|
[472] | 607 | template <> |
---|
[686] | 608 | void CONetCDF4::addAttribute(const StdString& name, const long int& value, const StdString* varname) |
---|
[472] | 609 | { |
---|
| 610 | int grpid = this->getCurrentGroup(); |
---|
| 611 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 612 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[472] | 613 | } |
---|
| 614 | |
---|
[686] | 615 | template <> |
---|
| 616 | void CONetCDF4::addAttribute(const StdString& name, const CArray<long int,1>& value, const StdString* varname) |
---|
[472] | 617 | { |
---|
| 618 | int grpid = this->getCurrentGroup(); |
---|
| 619 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 620 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 621 | } |
---|
| 622 | |
---|
[686] | 623 | //--------------------------------------------------------------- |
---|
[498] | 624 | |
---|
[686] | 625 | void CONetCDF4::getWriteDataInfos(const StdString& name, StdSize record, StdSize& array_size, |
---|
| 626 | std::vector<StdSize>& sstart, |
---|
| 627 | std::vector<StdSize>& scount, |
---|
| 628 | const std::vector<StdSize>* start, |
---|
| 629 | const std::vector<StdSize>* count) |
---|
[498] | 630 | { |
---|
[266] | 631 | std::vector<std::size_t> sizes = this->getDimensions(name); |
---|
[857] | 632 | if (sizes.size()==0) |
---|
[266] | 633 | { |
---|
[2264] | 634 | |
---|
| 635 | if ((start != NULL) && (count != NULL) && start->size()==1 && count->size()==1) // pur scalar case |
---|
| 636 | array_size*=(*count)[0] ; |
---|
| 637 | else array_size=1 ; |
---|
[266] | 638 | } |
---|
[857] | 639 | else |
---|
| 640 | { |
---|
| 641 | std::vector<std::string> iddims = this->getDimensionsIdList (&name); |
---|
| 642 | std::vector<std::size_t>::const_iterator |
---|
| 643 | it = sizes.begin(), end = sizes.end(); |
---|
| 644 | int i = 0; |
---|
[219] | 645 | |
---|
[857] | 646 | if (iddims.begin()->compare(timeCounterName) == 0) |
---|
| 647 | { |
---|
| 648 | sstart.push_back(record); |
---|
| 649 | scount.push_back(1); |
---|
[2264] | 650 | if ((start == NULL) && (count == NULL)) i++; |
---|
| 651 | it++; |
---|
| 652 | if (it==end) |
---|
| 653 | { |
---|
| 654 | if ((start != NULL) && (count != NULL) && start->size()==1 && count->size()==1) // pur scalar case |
---|
| 655 | { |
---|
| 656 | scount[0]=(*count)[0] ; |
---|
| 657 | array_size *= (*count)[0]; |
---|
| 658 | } |
---|
| 659 | } |
---|
[857] | 660 | } |
---|
[2264] | 661 | |
---|
[857] | 662 | for (;it != end; it++) |
---|
| 663 | { |
---|
| 664 | if ((start != NULL) && (count != NULL)) |
---|
| 665 | { |
---|
| 666 | sstart.push_back((*start)[i]); |
---|
| 667 | scount.push_back((*count)[i]); |
---|
| 668 | array_size *= (*count)[i]; |
---|
| 669 | i++; |
---|
| 670 | } |
---|
| 671 | else |
---|
| 672 | { |
---|
| 673 | sstart.push_back(0); |
---|
| 674 | scount.push_back(sizes[i]); |
---|
| 675 | array_size *= sizes[i]; |
---|
| 676 | i++; |
---|
| 677 | } |
---|
| 678 | } |
---|
| 679 | |
---|
[219] | 680 | } |
---|
| 681 | } |
---|
[498] | 682 | |
---|
[857] | 683 | |
---|
[219] | 684 | template <> |
---|
[686] | 685 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 686 | const std::vector<StdSize>& sstart, |
---|
| 687 | const std::vector<StdSize>& scount, const double* data) |
---|
[219] | 688 | { |
---|
[686] | 689 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
[219] | 690 | } |
---|
[498] | 691 | |
---|
[219] | 692 | //--------------------------------------------------------------- |
---|
[498] | 693 | |
---|
[219] | 694 | template <> |
---|
[686] | 695 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 696 | const std::vector<StdSize>& sstart, |
---|
[1158] | 697 | const std::vector<StdSize>& scount, char* data) |
---|
| 698 | { |
---|
| 699 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
| 700 | } |
---|
| 701 | |
---|
| 702 | template <> |
---|
| 703 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 704 | const std::vector<StdSize>& sstart, |
---|
[686] | 705 | const std::vector<StdSize>& scount, const int* data) |
---|
[219] | 706 | { |
---|
[686] | 707 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
[219] | 708 | } |
---|
| 709 | //--------------------------------------------------------------- |
---|
[498] | 710 | |
---|
[219] | 711 | template <> |
---|
[686] | 712 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 713 | const std::vector<StdSize>& sstart, |
---|
[1957] | 714 | const std::vector<StdSize>& scount, const size_t* data) |
---|
| 715 | { |
---|
| 716 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
| 717 | } |
---|
| 718 | //--------------------------------------------------------------- |
---|
| 719 | |
---|
| 720 | template <> |
---|
| 721 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 722 | const std::vector<StdSize>& sstart, |
---|
[686] | 723 | const std::vector<StdSize>& scount, const float* data) |
---|
[219] | 724 | { |
---|
[686] | 725 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
[219] | 726 | } |
---|
| 727 | |
---|
| 728 | //--------------------------------------------------------------- |
---|
| 729 | |
---|
[686] | 730 | void CONetCDF4::writeData(const CArray<int, 2>& data, const StdString& name) |
---|
[219] | 731 | { |
---|
| 732 | int grpid = this->getCurrentGroup(); |
---|
| 733 | int varid = this->getVariable(name); |
---|
[2264] | 734 | |
---|
[219] | 735 | StdSize array_size = 1; |
---|
| 736 | std::vector<StdSize> sstart, scount; |
---|
| 737 | |
---|
| 738 | this->getWriteDataInfos(name, 0, array_size, sstart, scount, NULL, NULL); |
---|
[1158] | 739 | |
---|
[369] | 740 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
---|
[1158] | 741 | |
---|
[219] | 742 | } |
---|
| 743 | |
---|
[686] | 744 | void CONetCDF4::writeTimeAxisData(const CArray<double, 1>& data, const StdString& name, |
---|
[413] | 745 | bool collective, StdSize record, bool isRoot) |
---|
| 746 | { |
---|
| 747 | int grpid = this->getCurrentGroup(); |
---|
| 748 | int varid = this->getVariable(name); |
---|
[498] | 749 | |
---|
[686] | 750 | map<int,size_t>::iterator it=timeAxis.find(varid); |
---|
| 751 | if (it == timeAxis.end()) timeAxis[varid] = record; |
---|
[498] | 752 | else |
---|
[413] | 753 | { |
---|
[686] | 754 | if (it->second >= record) return; |
---|
| 755 | else it->second =record; |
---|
[413] | 756 | } |
---|
[498] | 757 | |
---|
[413] | 758 | StdSize array_size = 1; |
---|
| 759 | std::vector<StdSize> sstart, scount; |
---|
[498] | 760 | |
---|
[413] | 761 | if (this->wmpi && collective) |
---|
[686] | 762 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
---|
[413] | 763 | if (this->wmpi && !collective) |
---|
[686] | 764 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
---|
[498] | 765 | |
---|
[413] | 766 | this->getWriteDataInfos(name, record, array_size, sstart, scount, NULL, NULL); |
---|
[1158] | 767 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
---|
| 768 | } |
---|
| 769 | |
---|
| 770 | void CONetCDF4::writeTimeAxisDataBounds(const CArray<double, 1>& data, const StdString& name, |
---|
| 771 | bool collective, StdSize record, bool isRoot) |
---|
| 772 | { |
---|
| 773 | int grpid = this->getCurrentGroup(); |
---|
| 774 | int varid = this->getVariable(name); |
---|
| 775 | |
---|
| 776 | map<int,size_t>::iterator it=timeAxis.find(varid); |
---|
| 777 | if (it == timeAxis.end()) timeAxis[varid] = record; |
---|
| 778 | else |
---|
[686] | 779 | { |
---|
[1158] | 780 | if (it->second >= record) return; |
---|
| 781 | else it->second =record; |
---|
[686] | 782 | } |
---|
[1158] | 783 | |
---|
| 784 | StdSize array_size = 1; |
---|
| 785 | std::vector<StdSize> sstart, scount; |
---|
| 786 | |
---|
| 787 | if (this->wmpi && collective) |
---|
| 788 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
---|
| 789 | if (this->wmpi && !collective) |
---|
| 790 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
---|
| 791 | |
---|
| 792 | this->getWriteDataInfos(name, record, array_size, sstart, scount, NULL, NULL); |
---|
[413] | 793 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
---|
| 794 | } |
---|
| 795 | |
---|
[1158] | 796 | |
---|
[219] | 797 | //--------------------------------------------------------------- |
---|
[498] | 798 | |
---|
[686] | 799 | bool CONetCDF4::varExist(const StdString& varname) |
---|
[219] | 800 | { |
---|
| 801 | int grpid = this->getCurrentGroup(); |
---|
[686] | 802 | return CNetCdfInterface::isVarExisted(grpid, varname); |
---|
[219] | 803 | } |
---|
| 804 | |
---|
[878] | 805 | bool CONetCDF4::dimExist(const StdString& dimname) |
---|
| 806 | { |
---|
| 807 | int grpid = this->getCurrentGroup(); |
---|
| 808 | return CNetCdfInterface::isDimExisted(grpid, dimname); |
---|
| 809 | } |
---|
| 810 | |
---|
[286] | 811 | void CONetCDF4::sync(void) |
---|
| 812 | { |
---|
[686] | 813 | CNetCdfInterface::sync(this->ncidp); |
---|
[498] | 814 | } |
---|
[219] | 815 | ///-------------------------------------------------------------- |
---|
[337] | 816 | } // namespace xios |
---|