1 | /* |
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2 | This file is part of netcdf-4, a netCDF-like interface for HDF5, or a |
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3 | HDF5 backend for netCDF, depending on your point of view. |
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4 | |
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5 | This file handles the nc4 variable functions. |
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6 | |
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7 | Copyright 2003-2006, University Corporation for Atmospheric |
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8 | Research. See COPYRIGHT file for copying and redistribution |
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9 | conditions. |
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10 | */ |
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11 | |
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12 | #include <nc4internal.h> |
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13 | #include "nc4dispatch.h" |
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14 | #include <math.h> |
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15 | |
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16 | #ifdef USE_PNETCDF |
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17 | #include <pnetcdf.h> |
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18 | #endif |
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19 | |
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20 | /* Min and max deflate levels tolerated by HDF5. */ |
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21 | #define MIN_DEFLATE_LEVEL 0 |
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22 | #define MAX_DEFLATE_LEVEL 9 |
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23 | |
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24 | /* This is to track opened HDF5 objects to make sure they are |
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25 | * closed. */ |
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26 | #ifdef EXTRA_TESTS |
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27 | extern int num_plists; |
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28 | #endif /* EXTRA_TESTS */ |
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29 | |
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30 | /* One meg is the minimum buffer size. */ |
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31 | #define ONE_MEG 1048576 |
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32 | |
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33 | /* Szip options. */ |
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34 | #define NC_SZIP_EC_OPTION_MASK 4 |
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35 | #define NC_SZIP_NN_OPTION_MASK 32 |
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36 | #define NC_SZIP_MAX_PIXELS_PER_BLOCK 32 |
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37 | |
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38 | int nc4_get_default_fill_value(NC_TYPE_INFO_T *type_info, void *fill_value); |
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39 | |
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40 | |
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41 | /* If the HDF5 dataset for this variable is open, then close it and |
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42 | * reopen it, with the perhaps new settings for chunk caching. */ |
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43 | int |
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44 | nc4_reopen_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var) |
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45 | { |
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46 | hid_t access_pid; |
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47 | |
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48 | if (var->hdf_datasetid) |
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49 | { |
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50 | if ((access_pid = H5Pcreate(H5P_DATASET_ACCESS)) < 0) |
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51 | return NC_EHDFERR; |
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52 | #ifdef EXTRA_TESTS |
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53 | num_plists++; |
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54 | #endif |
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55 | if (H5Pset_chunk_cache(access_pid, var->chunk_cache_nelems, |
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56 | var->chunk_cache_size, |
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57 | var->chunk_cache_preemption) < 0) |
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58 | return NC_EHDFERR; |
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59 | if (H5Dclose(var->hdf_datasetid) < 0) |
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60 | return NC_EHDFERR; |
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61 | if ((var->hdf_datasetid = H5Dopen2(grp->hdf_grpid, var->name, |
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62 | access_pid)) < 0) |
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63 | return NC_EHDFERR; |
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64 | if (H5Pclose(access_pid) < 0) |
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65 | return NC_EHDFERR; |
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66 | #ifdef EXTRA_TESTS |
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67 | num_plists--; |
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68 | #endif |
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69 | |
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70 | if (var->dimscale) |
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71 | var->dim[0]->hdf_dimscaleid = var->hdf_datasetid; |
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72 | } |
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73 | |
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74 | return NC_NOERR; |
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75 | } |
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76 | |
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77 | /* Set chunk cache size for a variable. */ |
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78 | int |
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79 | NC4_set_var_chunk_cache(int ncid, int varid, size_t size, size_t nelems, |
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80 | float preemption) |
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81 | { |
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82 | NC_FILE_INFO_T *nc; |
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83 | NC_GRP_INFO_T *grp; |
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84 | NC_HDF5_FILE_INFO_T *h5; |
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85 | NC_VAR_INFO_T *var; |
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86 | int retval; |
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87 | |
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88 | /* Check input for validity. */ |
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89 | if (preemption < 0 || preemption > 1) |
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90 | return NC_EINVAL; |
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91 | |
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92 | /* Find info for this file and group, and set pointer to each. */ |
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93 | if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) |
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94 | return retval; |
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95 | |
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96 | /* An attempt to do any of these things on a netCDF-3 file is |
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97 | * ignored with no error. */ |
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98 | if (!h5) |
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99 | return NC_NOERR; |
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100 | |
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101 | assert(nc && grp && h5); |
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102 | |
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103 | /* Find the var. */ |
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104 | for (var = grp->var; var; var = var->next) |
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105 | if (var->varid == varid) |
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106 | break; |
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107 | if (!var) |
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108 | return NC_ENOTVAR; |
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109 | |
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110 | /* Set the values. */ |
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111 | var->chunk_cache_size = size; |
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112 | var->chunk_cache_nelems = nelems; |
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113 | var->chunk_cache_preemption = preemption; |
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114 | |
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115 | if ((retval = nc4_reopen_dataset(grp, var))) |
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116 | return retval; |
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117 | |
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118 | return NC_NOERR; |
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119 | } |
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120 | |
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121 | /* Need this version for fortran. Accept negative numbers to leave |
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122 | * settings as they are. */ |
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123 | int |
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124 | nc_set_var_chunk_cache_ints(int ncid, int varid, int size, int nelems, |
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125 | int preemption) |
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126 | { |
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127 | size_t real_size = H5D_CHUNK_CACHE_NBYTES_DEFAULT; |
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128 | size_t real_nelems = H5D_CHUNK_CACHE_NSLOTS_DEFAULT; |
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129 | float real_preemption = H5D_CHUNK_CACHE_W0_DEFAULT; |
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130 | |
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131 | if (size >= 0) |
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132 | real_size = size * MEGABYTE; |
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133 | |
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134 | if (nelems >= 0) |
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135 | real_nelems = nelems; |
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136 | |
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137 | if (preemption >= 0) |
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138 | real_preemption = preemption / 100.; |
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139 | |
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140 | return nc_set_var_chunk_cache(ncid, varid, real_size, real_nelems, |
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141 | real_preemption); |
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142 | } |
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143 | |
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144 | /* Get chunk cache size for a variable. */ |
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145 | int |
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146 | NC4_get_var_chunk_cache(int ncid, int varid, size_t *sizep, |
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147 | size_t *nelemsp, float *preemptionp) |
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148 | { |
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149 | NC_FILE_INFO_T *nc; |
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150 | NC_GRP_INFO_T *grp; |
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151 | NC_HDF5_FILE_INFO_T *h5; |
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152 | NC_VAR_INFO_T *var; |
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153 | int retval; |
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154 | |
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155 | /* Find info for this file and group, and set pointer to each. */ |
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156 | if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) |
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157 | return retval; |
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158 | |
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159 | /* Attempting to do any of these things on a netCDF-3 file produces |
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160 | * an error. */ |
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161 | if (!h5) |
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162 | return NC_ENOTNC4; |
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163 | |
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164 | assert(nc && grp && h5); |
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165 | |
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166 | /* Find the var. */ |
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167 | for (var = grp->var; var; var = var->next) |
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168 | if (var->varid == varid) |
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169 | break; |
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170 | if (!var) |
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171 | return NC_ENOTVAR; |
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172 | |
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173 | /* Give the user what they want. */ |
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174 | if (sizep) |
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175 | *sizep = var->chunk_cache_size; |
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176 | if (nelemsp) |
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177 | *nelemsp = var->chunk_cache_nelems; |
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178 | if (preemptionp) |
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179 | *preemptionp = var->chunk_cache_preemption; |
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180 | |
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181 | return NC_NOERR; |
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182 | } |
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183 | |
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184 | /* Get chunk cache size for a variable. */ |
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185 | int |
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186 | nc_get_var_chunk_cache_ints(int ncid, int varid, int *sizep, |
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187 | int *nelemsp, int *preemptionp) |
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188 | { |
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189 | size_t real_size, real_nelems; |
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190 | float real_preemption; |
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191 | int ret; |
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192 | |
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193 | if ((ret = nc_get_var_chunk_cache(ncid, varid, &real_size, |
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194 | &real_nelems, &real_preemption))) |
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195 | return ret; |
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196 | |
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197 | if (sizep) |
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198 | *sizep = real_size / MEGABYTE; |
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199 | if (nelemsp) |
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200 | *nelemsp = (int)real_nelems; |
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201 | if(preemptionp) |
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202 | *preemptionp = (int)(real_preemption * 100); |
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203 | |
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204 | return NC_NOERR; |
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205 | } |
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206 | |
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207 | /* Check a set of chunksizes to see if they add up to a chunk that is too big. */ |
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208 | static int |
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209 | check_chunksizes(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, const size_t *chunksizes) |
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210 | { |
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211 | NC_TYPE_INFO_T *type_info; |
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212 | float total; |
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213 | size_t type_len; |
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214 | int d; |
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215 | int retval; |
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216 | |
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217 | if ((retval = nc4_get_typelen_mem(grp->file->nc4_info, var->xtype, 0, &type_len))) |
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218 | return retval; |
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219 | if ((retval = nc4_find_type(grp->file->nc4_info, var->xtype, &type_info))) |
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220 | return retval; |
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221 | if (type_info && type_info->class == NC_VLEN) |
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222 | total = sizeof(hvl_t); |
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223 | else |
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224 | total = type_len; |
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225 | for (d = 0; d < var->ndims; d++) |
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226 | { |
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227 | if (chunksizes[d] < 1) |
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228 | return NC_EINVAL; |
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229 | total *= chunksizes[d]; |
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230 | } |
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231 | |
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232 | if (total > NC_MAX_UINT) |
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233 | return NC_EBADCHUNK; |
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234 | |
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235 | return NC_NOERR; |
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236 | } |
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237 | |
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238 | /* Find the default chunk nelems (i.e. length of chunk along each |
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239 | * dimension). */ |
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240 | static int |
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241 | nc4_find_default_chunksizes2(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var) |
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242 | { |
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243 | int d; |
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244 | size_t type_size, max_len = 0; |
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245 | float num_values = 1, num_set = 0; |
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246 | int retval; |
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247 | #ifdef LOGGING |
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248 | int max_dim; |
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249 | float total_chunk_size; |
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250 | #endif |
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251 | |
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252 | if (var->type_info->nc_typeid == NC_STRING) |
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253 | type_size = sizeof(char *); |
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254 | else |
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255 | type_size = var->type_info->size; |
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256 | |
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257 | /* Later this will become the total number of bytes in the default |
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258 | * chunk. */ |
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259 | #ifdef LOGGING |
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260 | total_chunk_size = type_size; |
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261 | #endif |
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262 | |
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263 | /* How many values in the variable (or one record, if there are |
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264 | * unlimited dimensions); which is the largest dimension, and how |
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265 | * long is it? */ |
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266 | for (d = 0; d < var->ndims; d++) |
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267 | { |
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268 | assert(var->dim[d]); |
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269 | if (var->dim[d]->len) |
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270 | num_values *= (float)var->dim[d]->len; |
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271 | else |
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272 | num_set++; |
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273 | |
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274 | if (var->dim[d]->len > max_len) |
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275 | { |
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276 | max_len = var->dim[d]->len; |
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277 | #ifdef LOGGING |
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278 | max_dim = d; |
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279 | #endif |
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280 | } |
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281 | LOG((4, "d = %d max_dim %d max_len %ld num_values %f", d, max_dim, max_len, |
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282 | num_values)); |
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283 | } |
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284 | |
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285 | /* If a dim is several orders of magnitude smaller than the max |
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286 | * dimension, set it's chunk size to the full extent of the smaller |
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287 | * dimension. */ |
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288 | #define NC_DIM_MULTIPLIER 10000 |
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289 | for (d = 0; d < var->ndims; d++) |
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290 | if (var->dim[d]->unlimited) |
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291 | var->chunksizes[d] = 1; |
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292 | else if (!var->dim[d]->unlimited && var->dim[d]->len * NC_DIM_MULTIPLIER < max_len) |
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293 | { |
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294 | var->chunksizes[d] = var->dim[d]->len; |
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295 | num_set++; |
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296 | } |
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297 | |
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298 | /* Pick a chunk length for each dimension, if one has not already |
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299 | * been picked above. */ |
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300 | for (d = 0; d < var->ndims; d++) |
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301 | if (!var->chunksizes[d]) |
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302 | { |
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303 | size_t suggested_size; |
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304 | suggested_size = (pow((double)DEFAULT_CHUNK_SIZE/(num_values * type_size), |
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305 | 1/(double)(var->ndims - num_set)) * var->dim[d]->len - .5); |
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306 | if (suggested_size > var->dim[d]->len) |
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307 | suggested_size = var->dim[d]->len; |
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308 | var->chunksizes[d] = suggested_size ? suggested_size : 1; |
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309 | LOG((4, "nc_def_var_nc4: name %s dim %d DEFAULT_CHUNK_SIZE %d num_values %f type_size %d " |
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310 | "chunksize %ld", var->name, d, DEFAULT_CHUNK_SIZE, num_values, type_size, var->chunksizes[d])); |
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311 | } |
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312 | |
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313 | /* Find total chunk size. */ |
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314 | #ifdef LOGGING |
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315 | for (d = 0; d < var->ndims; d++) |
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316 | total_chunk_size *= var->chunksizes[d]; |
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317 | LOG((4, "total_chunk_size %f", total_chunk_size)); |
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318 | #endif |
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319 | |
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320 | /* But did this add up to a chunk that is too big? */ |
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321 | retval = check_chunksizes(grp, var, var->chunksizes); |
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322 | if (retval) |
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323 | { |
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324 | /* Other error? */ |
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325 | if (retval != NC_EBADCHUNK) |
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326 | return retval; |
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327 | |
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328 | /* Chunk is too big! Reduce each dimension by half and try again. */ |
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329 | for ( ; retval == NC_EBADCHUNK; retval = check_chunksizes(grp, var, var->chunksizes)) |
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330 | for (d = 0; d < var->ndims; d++) |
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331 | var->chunksizes[d] = var->chunksizes[d]/2 ? var->chunksizes[d]/2 : 1; |
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332 | } |
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333 | |
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334 | /* Do we have any big data overhangs? They can be dangerous to |
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335 | * babies, the elderly, or confused campers who have had too much |
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336 | * beer. */ |
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337 | for (d = 0; d < var->ndims; d++) |
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338 | { |
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339 | int num_chunks; |
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340 | size_t overhang; |
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341 | assert(var->chunksizes[d] > 0); |
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342 | num_chunks = (var->dim[d]->len + var->chunksizes[d] - 1) / var->chunksizes[d]; |
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343 | if(num_chunks > 0) { |
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344 | overhang = (num_chunks * var->chunksizes[d]) - var->dim[d]->len; |
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345 | var->chunksizes[d] -= overhang / num_chunks; |
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346 | } |
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347 | } |
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348 | |
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349 | return NC_NOERR; |
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350 | } |
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351 | |
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352 | /* This is called when a new netCDF-4 variable is defined. Break it |
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353 | * down! */ |
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354 | static int |
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355 | nc_def_var_nc4(int ncid, const char *name, nc_type xtype, |
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356 | int ndims, const int *dimidsp, int *varidp) |
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357 | { |
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358 | NC_GRP_INFO_T *grp; |
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359 | NC_VAR_INFO_T *var; |
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360 | NC_DIM_INFO_T *dim; |
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361 | NC_HDF5_FILE_INFO_T *h5; |
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362 | NC_TYPE_INFO_T *type_info; |
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363 | char norm_name[NC_MAX_NAME + 1]; |
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364 | int new_varid = 0; |
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365 | int num_unlim = 0; |
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366 | int d; |
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367 | size_t num_values = 1; |
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368 | int retval; |
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369 | |
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370 | /* Find info for this file and group, and set pointer to each. */ |
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371 | if ((retval = nc4_find_grp_h5(ncid, &grp, &h5))) |
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372 | return retval; |
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373 | assert(grp && h5); |
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374 | |
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375 | /* If it's not in define mode, strict nc3 files error out, |
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376 | * otherwise switch to define mode. */ |
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377 | if (!(h5->flags & NC_INDEF)) |
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378 | { |
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379 | if (h5->cmode & NC_CLASSIC_MODEL) |
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380 | return NC_ENOTINDEFINE; |
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381 | if ((retval = NC4_redef(ncid))) |
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382 | return retval; |
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383 | } |
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384 | |
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385 | /* Check and normalize the name. */ |
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386 | if ((retval = nc4_check_name(name, norm_name))) |
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387 | return retval; |
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388 | |
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389 | /* Not a Type is, well, not a type.*/ |
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390 | if (xtype == NC_NAT) |
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391 | return NC_EBADTYPE; |
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392 | |
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393 | /* For classic files, only classic types are allowed. */ |
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394 | if (h5->cmode & NC_CLASSIC_MODEL && xtype > NC_DOUBLE) |
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395 | return NC_ESTRICTNC3; |
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396 | |
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397 | /* If this is a user defined type, find it. */ |
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398 | if (xtype > NC_STRING) |
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399 | if (nc4_find_type(grp->file->nc4_info, xtype, &type_info)) |
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400 | return NC_EBADTYPE; |
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401 | |
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402 | /* cast needed for braindead systems with signed size_t */ |
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403 | if((unsigned long) ndims > X_INT_MAX) /* Backward compat */ |
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404 | return NC_EINVAL; |
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405 | |
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406 | /* Classic model files have a limit on number of vars. */ |
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407 | if(h5->cmode & NC_CLASSIC_MODEL && h5->nvars >= NC_MAX_VARS) |
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408 | return NC_EMAXVARS; |
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409 | |
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410 | /* Check that this name is not in use as a var, grp, or type. */ |
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411 | if ((retval = nc4_check_dup_name(grp, norm_name))) |
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412 | return retval; |
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413 | |
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414 | /* If the file is read-only, return an error. */ |
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415 | if (h5->no_write) |
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416 | return NC_EPERM; |
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417 | |
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418 | /* Get the new varid. */ |
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419 | for (var = grp->var; var; var = var->next) |
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420 | new_varid++; |
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421 | |
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422 | /* Check all the dimids to make sure they exist. */ |
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423 | for (d = 0; d < ndims; d++) |
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424 | { |
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425 | if ((retval = nc4_find_dim(grp, dimidsp[d], &dim, NULL))) |
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426 | return retval; |
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427 | if (dim->unlimited) |
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428 | num_unlim++; |
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429 | else |
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430 | num_values *= dim->len; |
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431 | } |
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432 | |
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433 | /* These degrubbing messages sure are handy! */ |
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434 | LOG((3, "nc_def_var_nc4: name %s type %d ndims %d", norm_name, xtype, ndims)); |
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435 | #ifdef LOGGING |
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436 | { |
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437 | int dd; |
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438 | for (dd = 0; dd < ndims; dd++) |
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439 | LOG((4, "dimid[%d] %d", dd, dimidsp[dd])); |
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440 | } |
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441 | #endif |
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442 | |
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443 | /* Add the var to the end of the list. */ |
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444 | if ((retval = nc4_var_list_add(&grp->var, &var))) |
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445 | return retval; |
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446 | |
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447 | /* Now fill in the values in the var info structure. */ |
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448 | if (!(var->name = malloc((strlen(norm_name) + 1) * sizeof(char)))) |
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449 | return NC_ENOMEM; |
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450 | strcpy(var->name, norm_name); |
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451 | var->varid = grp->nvars++; |
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452 | var->xtype = xtype; |
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453 | var->ndims = ndims; |
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454 | var->dirty++; |
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455 | |
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456 | /* If this is a user-defined type, there is a type_info stuct with |
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457 | * all the type information. For atomic types, fake up a type_info |
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458 | * struct. */ |
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459 | if (xtype > NC_STRING) |
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460 | var->type_info = type_info; |
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461 | else |
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462 | { |
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463 | if (!(var->type_info = calloc(1, sizeof(NC_TYPE_INFO_T)))) |
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464 | return NC_ENOMEM; |
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465 | var->type_info->nc_typeid = xtype; |
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466 | if ((retval = nc4_get_hdf_typeid(h5, var->xtype, &var->type_info->hdf_typeid, |
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467 | var->type_info->endianness))) |
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468 | return retval; |
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469 | if ((var->type_info->native_typeid = H5Tget_native_type(var->type_info->hdf_typeid, |
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470 | H5T_DIR_DEFAULT)) < 0) |
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471 | return NC_EHDFERR; |
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472 | if ((retval = nc4_get_typelen_mem(h5, var->type_info->nc_typeid, 0, |
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473 | &var->type_info->size))) |
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474 | return retval; |
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475 | } |
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476 | if (!num_unlim) |
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477 | var->contiguous = 1; |
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478 | |
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479 | /* Allocate space for dimension information. */ |
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480 | if (ndims) |
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481 | { |
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482 | if (!(var->dim = calloc(ndims, sizeof(NC_DIM_INFO_T *)))) |
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483 | return NC_ENOMEM; |
---|
484 | if (!(var->dimids = calloc(ndims, sizeof(int)))) |
---|
485 | return NC_ENOMEM; |
---|
486 | } |
---|
487 | |
---|
488 | /* At the same time, check to see if this is a coordinate |
---|
489 | * variable. If so, it will have the same name as one of its |
---|
490 | * dimensions. If it is a coordinate var, is it a coordinate var in |
---|
491 | * the same group as the dim? */ |
---|
492 | for (d = 0; d < ndims; d++) |
---|
493 | { |
---|
494 | NC_GRP_INFO_T *dim_grp; |
---|
495 | if ((retval = nc4_find_dim(grp, dimidsp[d], &dim, &dim_grp))) |
---|
496 | return retval; |
---|
497 | if (strcmp(dim->name, norm_name) == 0 && dim_grp == grp && d == 0) |
---|
498 | { |
---|
499 | var->dimscale++; |
---|
500 | dim->coord_var = var; |
---|
501 | dim->coord_var_in_grp++; |
---|
502 | } |
---|
503 | var->dimids[d] = dimidsp[d]; |
---|
504 | var->dim[d] = dim; |
---|
505 | } |
---|
506 | |
---|
507 | /* Determine default chunksizes for this variable. (Even for |
---|
508 | * variables which may be contiguous. */ |
---|
509 | LOG((4, "allocating array of %d size_t to hold chunksizes for var %s", |
---|
510 | var->ndims, var->name)); |
---|
511 | if (var->ndims) |
---|
512 | if (!(var->chunksizes = calloc(var->ndims, sizeof(size_t)))) |
---|
513 | return NC_ENOMEM; |
---|
514 | |
---|
515 | if ((retval = nc4_find_default_chunksizes2(grp, var))) |
---|
516 | return retval; |
---|
517 | |
---|
518 | /* Is this a variable with a chunksize greater than the current |
---|
519 | * cache size? */ |
---|
520 | if ((retval = nc4_adjust_var_cache(grp, var))) |
---|
521 | return retval; |
---|
522 | |
---|
523 | /* If the user names this variable the same as a dimension, but |
---|
524 | * doesn't use that dimension first in its list of dimension ids, |
---|
525 | * is not a coordinate variable. I need to change its HDF5 name, |
---|
526 | * because the dimension will cause a HDF5 dataset to be created, |
---|
527 | * and this var has the same name. */ |
---|
528 | for (dim = grp->dim; dim; dim = dim->next) |
---|
529 | if (!strcmp(dim->name, norm_name) && |
---|
530 | (!var->ndims || dimidsp[0] != dim->dimid)) |
---|
531 | { |
---|
532 | /* Set a different hdf5 name for this variable to avoid name |
---|
533 | * clash. */ |
---|
534 | if (strlen(norm_name) + strlen(NON_COORD_PREPEND) > NC_MAX_NAME) |
---|
535 | return NC_EMAXNAME; |
---|
536 | if (!(var->hdf5_name = malloc((strlen(NON_COORD_PREPEND) + |
---|
537 | strlen(norm_name) + 1) * sizeof(char)))) |
---|
538 | return NC_ENOMEM; |
---|
539 | |
---|
540 | sprintf(var->hdf5_name, "%s%s", NON_COORD_PREPEND, norm_name); |
---|
541 | } |
---|
542 | |
---|
543 | /* If this is a coordinate var, it is marked as a HDF5 dimension |
---|
544 | * scale. (We found dim above.) Otherwise, allocate space to |
---|
545 | * remember whether dimension scales have been attached to each |
---|
546 | * dimension. */ |
---|
547 | if (!var->dimscale && ndims) |
---|
548 | if (ndims && !(var->dimscale_attached = calloc(ndims, sizeof(int)))) |
---|
549 | return NC_ENOMEM; |
---|
550 | |
---|
551 | /* Return the varid. */ |
---|
552 | if (varidp) |
---|
553 | *varidp = var->varid; |
---|
554 | LOG((4, "new varid %d", var->varid)); |
---|
555 | |
---|
556 | return retval; |
---|
557 | } |
---|
558 | |
---|
559 | /* Create a new variable to hold user data. This is what it's all |
---|
560 | * about baby! */ |
---|
561 | int |
---|
562 | NC4_def_var(int ncid, const char *name, nc_type xtype, int ndims, |
---|
563 | const int *dimidsp, int *varidp) |
---|
564 | { |
---|
565 | NC_FILE_INFO_T *nc; |
---|
566 | |
---|
567 | LOG((2, "nc_def_var: ncid 0x%x name %s xtype %d ndims %d", |
---|
568 | ncid, name, xtype, ndims)); |
---|
569 | |
---|
570 | /* If there are dimensions, I need their ids. */ |
---|
571 | if (ndims && !dimidsp) |
---|
572 | return NC_EINVAL; |
---|
573 | |
---|
574 | /* Find metadata for this file. */ |
---|
575 | if (!(nc = nc4_find_nc_file(ncid))) |
---|
576 | return NC_EBADID; |
---|
577 | |
---|
578 | #ifdef USE_PNETCDF |
---|
579 | /* Take care of files created/opened with parallel-netcdf library. */ |
---|
580 | if (nc->pnetcdf_file) |
---|
581 | { |
---|
582 | int ret; |
---|
583 | |
---|
584 | ret = ncmpi_def_var(nc->int_ncid, name, xtype, ndims, |
---|
585 | dimidsp, varidp); |
---|
586 | nc->pnetcdf_ndims[*varidp] = ndims; |
---|
587 | return ret; |
---|
588 | } |
---|
589 | #endif /* USE_PNETCDF */ |
---|
590 | |
---|
591 | /* Netcdf-3 cases handled by dispatch layer. */ |
---|
592 | assert(nc->nc4_info); |
---|
593 | |
---|
594 | /* Handle netcdf-4 cases. */ |
---|
595 | return nc_def_var_nc4(ncid, name, xtype, ndims, dimidsp, varidp); |
---|
596 | } |
---|
597 | |
---|
598 | /* Get all the information about a variable. Pass NULL for whatever |
---|
599 | * you don't care about. This is an internal function, not exposed to |
---|
600 | * the user. */ |
---|
601 | int |
---|
602 | NC4_inq_var_all(int ncid, int varid, char *name, nc_type *xtypep, |
---|
603 | int *ndimsp, int *dimidsp, int *nattsp, |
---|
604 | int *shufflep, int *deflatep, int *deflate_levelp, |
---|
605 | int *fletcher32p, int *contiguousp, size_t *chunksizesp, |
---|
606 | int *no_fill, void *fill_valuep, int *endiannessp, |
---|
607 | int *options_maskp, int *pixels_per_blockp) |
---|
608 | { |
---|
609 | NC_FILE_INFO_T *nc; |
---|
610 | NC_GRP_INFO_T *grp; |
---|
611 | NC_HDF5_FILE_INFO_T *h5; |
---|
612 | NC_VAR_INFO_T *var; |
---|
613 | NC_ATT_INFO_T *att; |
---|
614 | int natts=0; |
---|
615 | size_t type_size; |
---|
616 | int d; |
---|
617 | int retval; |
---|
618 | |
---|
619 | LOG((2, "nc_inq_var_all: ncid 0x%x varid %d", ncid, varid)); |
---|
620 | |
---|
621 | /* Find info for this file and group, and set pointer to each. */ |
---|
622 | if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) |
---|
623 | return retval; |
---|
624 | assert(nc && grp && h5); |
---|
625 | |
---|
626 | #ifdef USE_PNETCDF |
---|
627 | /* Take care of files created/opened with parallel-netcdf library. */ |
---|
628 | if (nc->pnetcdf_file) |
---|
629 | return ncmpi_inq_var(nc->int_ncid, varid, name, xtypep, ndimsp, |
---|
630 | dimidsp, nattsp); |
---|
631 | #endif /* USE_PNETCDF */ |
---|
632 | |
---|
633 | /* Walk through the list of vars, and return the info about the one |
---|
634 | with a matching varid. If the varid is -1, find the global |
---|
635 | atts and call it a day. */ |
---|
636 | if (varid == NC_GLOBAL) |
---|
637 | { |
---|
638 | if (nattsp) |
---|
639 | { |
---|
640 | for (att = grp->att; att; att = att->next) |
---|
641 | natts++; |
---|
642 | *nattsp = natts; |
---|
643 | } |
---|
644 | return NC_NOERR; |
---|
645 | } |
---|
646 | |
---|
647 | /* Find the var. */ |
---|
648 | for (var = grp->var; var; var = var->next) |
---|
649 | if (var->varid == varid) |
---|
650 | break; |
---|
651 | |
---|
652 | /* Oh no! Maybe we couldn't find it (*sob*)! */ |
---|
653 | if (!var) |
---|
654 | return NC_ENOTVAR; |
---|
655 | |
---|
656 | /* Copy the data to the user's data buffers. */ |
---|
657 | if (name) |
---|
658 | strcpy(name, var->name); |
---|
659 | if (xtypep) |
---|
660 | *xtypep = var->xtype; |
---|
661 | if (ndimsp) |
---|
662 | *ndimsp = var->ndims; |
---|
663 | if (dimidsp) |
---|
664 | for (d = 0; d < var->ndims; d++) |
---|
665 | dimidsp[d] = var->dimids[d]; |
---|
666 | if (nattsp) |
---|
667 | { |
---|
668 | for (att = var->att; att; att = att->next) |
---|
669 | natts++; |
---|
670 | *nattsp = natts; |
---|
671 | } |
---|
672 | |
---|
673 | /* Chunking stuff. */ |
---|
674 | if (!var->contiguous && chunksizesp) |
---|
675 | for (d = 0; d < var->ndims; d++) |
---|
676 | { |
---|
677 | chunksizesp[d] = var->chunksizes[d]; |
---|
678 | LOG((4, "chunksizesp[%d]=%d", d, chunksizesp[d])); |
---|
679 | } |
---|
680 | |
---|
681 | if (contiguousp) |
---|
682 | *contiguousp = var->contiguous ? NC_CONTIGUOUS : NC_CHUNKED; |
---|
683 | |
---|
684 | /* Filter stuff. */ |
---|
685 | if (deflatep) |
---|
686 | *deflatep = var->deflate; |
---|
687 | if (deflate_levelp) |
---|
688 | *deflate_levelp = var->deflate_level; |
---|
689 | if (shufflep) |
---|
690 | *shufflep = var->shuffle; |
---|
691 | if (fletcher32p) |
---|
692 | *fletcher32p = var->fletcher32; |
---|
693 | if (options_maskp) |
---|
694 | *options_maskp = var->options_mask; |
---|
695 | if (pixels_per_blockp) |
---|
696 | *pixels_per_blockp = var->pixels_per_block; |
---|
697 | |
---|
698 | /* Fill value stuff. */ |
---|
699 | if (no_fill) |
---|
700 | *no_fill = var->no_fill; |
---|
701 | |
---|
702 | /* Don't do a thing with fill_valuep if no_fill mode is set for |
---|
703 | * this var, or if fill_valuep is NULL. */ |
---|
704 | if (!var->no_fill && fill_valuep) |
---|
705 | { |
---|
706 | /* Do we have a fill value for this var? */ |
---|
707 | if (var->fill_value) |
---|
708 | { |
---|
709 | if ((retval = nc4_get_typelen_mem(grp->file->nc4_info, var->xtype, 0, &type_size))) |
---|
710 | return retval; |
---|
711 | memcpy(fill_valuep, var->fill_value, type_size); |
---|
712 | } |
---|
713 | else |
---|
714 | { |
---|
715 | if ((retval = nc4_get_default_fill_value(var->type_info, fill_valuep))) |
---|
716 | return retval; |
---|
717 | } |
---|
718 | } |
---|
719 | |
---|
720 | /* Does the user want the endianness of this variable? */ |
---|
721 | if (endiannessp) |
---|
722 | *endiannessp = var->type_info->endianness; |
---|
723 | |
---|
724 | return NC_NOERR; |
---|
725 | } |
---|
726 | |
---|
727 | /* This functions sets extra stuff about a netCDF-4 variable which |
---|
728 | must be set before the enddef but after the def_var. This is an |
---|
729 | internal function, deliberately hidden from the user so that we can |
---|
730 | change the prototype of this functions without changing the API. */ |
---|
731 | static int |
---|
732 | nc_def_var_extra(int ncid, int varid, int *shuffle, int *deflate, |
---|
733 | int *deflate_level, int *fletcher32, int *contiguous, |
---|
734 | const size_t *chunksizes, int *no_fill, |
---|
735 | const void *fill_value, int *endianness, |
---|
736 | int *options_mask, int *pixels_per_block) |
---|
737 | { |
---|
738 | NC_FILE_INFO_T *nc; |
---|
739 | NC_GRP_INFO_T *grp; |
---|
740 | NC_HDF5_FILE_INFO_T *h5; |
---|
741 | NC_VAR_INFO_T *var; |
---|
742 | NC_DIM_INFO_T *dim; |
---|
743 | size_t type_size; |
---|
744 | int d; |
---|
745 | int retval; |
---|
746 | |
---|
747 | LOG((2, "nc_def_var_extra: ncid 0x%x varid %d", ncid, varid)); |
---|
748 | |
---|
749 | /* Find info for this file and group, and set pointer to each. */ |
---|
750 | if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) |
---|
751 | return retval; |
---|
752 | |
---|
753 | /* Attempting to do any of these things on a netCDF-3 file produces |
---|
754 | * an error. */ |
---|
755 | if (!h5) |
---|
756 | return NC_ENOTNC4; |
---|
757 | |
---|
758 | assert(nc && grp && h5); |
---|
759 | |
---|
760 | /* Find the var. */ |
---|
761 | for (var = grp->var; var; var = var->next) |
---|
762 | if (var->varid == varid) |
---|
763 | break; |
---|
764 | |
---|
765 | /* Oh no! Maybe we couldn't find it (*sob*)! */ |
---|
766 | if (!var) |
---|
767 | return NC_ENOTVAR; |
---|
768 | |
---|
769 | /* Can't turn on contiguous and deflate/fletcher32/szip. */ |
---|
770 | if (contiguous) |
---|
771 | if ((*contiguous != NC_CHUNKED && deflate) || |
---|
772 | (*contiguous != NC_CHUNKED && fletcher32) || |
---|
773 | (*contiguous != NC_CHUNKED && options_mask)) |
---|
774 | return NC_EINVAL; |
---|
775 | |
---|
776 | /* If the HDF5 dataset has already been created, then it is too |
---|
777 | * late to set all the extra stuff. */ |
---|
778 | if (var->created) |
---|
779 | return NC_ELATEDEF; |
---|
780 | |
---|
781 | /* Check compression options. */ |
---|
782 | if ((deflate && options_mask) || |
---|
783 | (deflate && !deflate_level) || |
---|
784 | (options_mask && !pixels_per_block)) |
---|
785 | return NC_EINVAL; |
---|
786 | |
---|
787 | /* Valid deflate level? */ |
---|
788 | if (deflate && deflate_level) |
---|
789 | { |
---|
790 | if (*deflate) |
---|
791 | if (*deflate_level < MIN_DEFLATE_LEVEL || |
---|
792 | *deflate_level > MAX_DEFLATE_LEVEL) |
---|
793 | return NC_EINVAL; |
---|
794 | if (var->options_mask) |
---|
795 | return NC_EINVAL; |
---|
796 | |
---|
797 | /* For scalars, just ignore attempt to deflate. */ |
---|
798 | if (!var->ndims) |
---|
799 | return NC_NOERR; |
---|
800 | |
---|
801 | /* Well, if we couldn't find any errors, I guess we have to take |
---|
802 | * the users settings. Darn! */ |
---|
803 | var->contiguous = 0; |
---|
804 | var->deflate = *deflate; |
---|
805 | if (*deflate) |
---|
806 | var->deflate_level = *deflate_level; |
---|
807 | LOG((3, "nc_def_var_extra: *deflate_level %d", *deflate_level)); |
---|
808 | } |
---|
809 | |
---|
810 | /* Szip in use? */ |
---|
811 | if (options_mask) |
---|
812 | { |
---|
813 | #ifndef USE_SZIP |
---|
814 | return NC_EINVAL; |
---|
815 | #endif |
---|
816 | if (var->deflate) |
---|
817 | return NC_EINVAL; |
---|
818 | if ((*options_mask != NC_SZIP_EC_OPTION_MASK) && |
---|
819 | (*options_mask != NC_SZIP_NN_OPTION_MASK)) |
---|
820 | return NC_EINVAL; |
---|
821 | if ((*pixels_per_block > NC_SZIP_MAX_PIXELS_PER_BLOCK) || |
---|
822 | (var->type_info->nc_typeid >= NC_STRING)) |
---|
823 | return NC_EINVAL; |
---|
824 | var->options_mask = *options_mask; |
---|
825 | var->pixels_per_block = *pixels_per_block; |
---|
826 | var->contiguous = 0; |
---|
827 | } |
---|
828 | |
---|
829 | /* Shuffle filter? */ |
---|
830 | if (shuffle) |
---|
831 | { |
---|
832 | var->shuffle = *shuffle; |
---|
833 | var->contiguous = 0; |
---|
834 | } |
---|
835 | |
---|
836 | /* Fltcher32 checksum error protection? */ |
---|
837 | if (fletcher32) |
---|
838 | { |
---|
839 | var->fletcher32 = *fletcher32; |
---|
840 | var->contiguous = 0; |
---|
841 | } |
---|
842 | |
---|
843 | /* Does the user want a contiguous dataset? Not so fast! Make sure |
---|
844 | * that there are no unlimited dimensions, and no filters in use |
---|
845 | * for this data. */ |
---|
846 | if (contiguous && *contiguous) |
---|
847 | { |
---|
848 | if (var->deflate || var->fletcher32 || var->shuffle || var->options_mask) |
---|
849 | return NC_EINVAL; |
---|
850 | |
---|
851 | for (d = 0; d < var->ndims; d++) |
---|
852 | { |
---|
853 | if ((retval = nc4_find_dim(grp, var->dimids[d], &dim, NULL))) |
---|
854 | return retval; |
---|
855 | if (dim->unlimited) |
---|
856 | return NC_EINVAL; |
---|
857 | } |
---|
858 | |
---|
859 | var->contiguous = NC_CONTIGUOUS; |
---|
860 | } |
---|
861 | |
---|
862 | /* Chunksizes anyone? */ |
---|
863 | if (contiguous && *contiguous == NC_CHUNKED) |
---|
864 | { |
---|
865 | var->contiguous = 0; |
---|
866 | |
---|
867 | /* If the user provided chunksizes, check that they are not too |
---|
868 | * big, and that their total size of chunk is less than 4 GB. */ |
---|
869 | if (chunksizes) |
---|
870 | { |
---|
871 | |
---|
872 | if ((retval = check_chunksizes(grp, var, chunksizes))) |
---|
873 | return retval; |
---|
874 | |
---|
875 | /* Set the chunksizes for this variable. */ |
---|
876 | for (d = 0; d < var->ndims; d++) |
---|
877 | var->chunksizes[d] = chunksizes[d]; |
---|
878 | } |
---|
879 | } |
---|
880 | |
---|
881 | /* Is this a variable with a chunksize greater than the current |
---|
882 | * cache size? */ |
---|
883 | if (var->contiguous == NC_CHUNKED && (chunksizes || deflate || contiguous)) |
---|
884 | { |
---|
885 | /* Determine default chunksizes for this variable. */ |
---|
886 | if (!var->chunksizes[0]) |
---|
887 | if ((retval = nc4_find_default_chunksizes2(grp, var))) |
---|
888 | return retval; |
---|
889 | |
---|
890 | /* Adjust the cache. */ |
---|
891 | if ((retval = nc4_adjust_var_cache(grp, var))) |
---|
892 | return retval; |
---|
893 | } |
---|
894 | |
---|
895 | /* Are we setting a fill modes? */ |
---|
896 | if (no_fill) |
---|
897 | { |
---|
898 | if (*no_fill) |
---|
899 | var->no_fill = 1; |
---|
900 | else |
---|
901 | var->no_fill = 0; |
---|
902 | } |
---|
903 | |
---|
904 | /* Are we setting a fill value? */ |
---|
905 | if (fill_value && !var->no_fill) |
---|
906 | { |
---|
907 | /* If fill value hasn't been set, allocate space. */ |
---|
908 | if ((retval = nc4_get_typelen_mem(h5, var->xtype, 0, &type_size))) |
---|
909 | return retval; |
---|
910 | if (!var->fill_value) |
---|
911 | if (!(var->fill_value = malloc(type_size))) |
---|
912 | return NC_ENOMEM; |
---|
913 | |
---|
914 | /* Copy the fill_value. */ |
---|
915 | LOG((4, "Copying fill value into metadata for variable %s", |
---|
916 | var->name)); |
---|
917 | memcpy(var->fill_value, fill_value, type_size); |
---|
918 | |
---|
919 | /* If there's a _FillValue attribute, delete it. */ |
---|
920 | retval = nc_del_att(ncid, varid, _FillValue); |
---|
921 | if (retval && retval != NC_ENOTATT) |
---|
922 | return retval; |
---|
923 | |
---|
924 | /* Create a _FillValue attribute. */ |
---|
925 | if ((retval = nc_put_att(ncid, varid, _FillValue, var->xtype, 1, fill_value))) |
---|
926 | return retval; |
---|
927 | } |
---|
928 | |
---|
929 | /* Is the user setting the endianness? */ |
---|
930 | if (endianness) |
---|
931 | var->type_info->endianness = *endianness; |
---|
932 | |
---|
933 | return NC_NOERR; |
---|
934 | } |
---|
935 | |
---|
936 | /* Set the deflate level for a var, lower is faster, higher is |
---|
937 | * better. Must be called after nc_def_var and before nc_enddef or any |
---|
938 | * functions which writes data to the file. */ |
---|
939 | int |
---|
940 | NC4_def_var_deflate(int ncid, int varid, int shuffle, int deflate, |
---|
941 | int deflate_level) |
---|
942 | { |
---|
943 | return nc_def_var_extra(ncid, varid, &shuffle, &deflate, |
---|
944 | &deflate_level, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL); |
---|
945 | } |
---|
946 | |
---|
947 | /* Set checksum for a var. This must be called after the nc_def_var |
---|
948 | * but before the nc_enddef. */ |
---|
949 | int |
---|
950 | NC4_def_var_fletcher32(int ncid, int varid, int fletcher32) |
---|
951 | { |
---|
952 | return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, &fletcher32, |
---|
953 | NULL, NULL, NULL, NULL, NULL, NULL, NULL); |
---|
954 | } |
---|
955 | |
---|
956 | /* Define chunking stuff for a var. This must be done after nc_def_var |
---|
957 | and before nc_enddef. |
---|
958 | |
---|
959 | Chunking is required in any dataset with one or more unlimited |
---|
960 | dimension in HDF5, or any dataset using a filter. |
---|
961 | |
---|
962 | Where chunksize is a pointer to an array of size ndims, with the |
---|
963 | chunksize in each dimension. |
---|
964 | */ |
---|
965 | int |
---|
966 | NC4_def_var_chunking(int ncid, int varid, int contiguous, const size_t *chunksizesp) |
---|
967 | { |
---|
968 | return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, |
---|
969 | &contiguous, chunksizesp, NULL, NULL, NULL, NULL, NULL); |
---|
970 | } |
---|
971 | |
---|
972 | /* Inquire about chunking stuff for a var. This is a private, |
---|
973 | * undocumented function, used by the f77 API to avoid size_t |
---|
974 | * problems. */ |
---|
975 | int |
---|
976 | nc_inq_var_chunking_ints(int ncid, int varid, int *contiguousp, int *chunksizesp) |
---|
977 | { |
---|
978 | NC_FILE_INFO_T *nc; |
---|
979 | NC_GRP_INFO_T *grp; |
---|
980 | NC_HDF5_FILE_INFO_T *h5; |
---|
981 | NC_VAR_INFO_T *var; |
---|
982 | size_t *cs = NULL; |
---|
983 | int i, retval; |
---|
984 | |
---|
985 | /* Find this ncid's file info. */ |
---|
986 | if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) |
---|
987 | return retval; |
---|
988 | assert(nc); |
---|
989 | |
---|
990 | /* Must be netcdf-4. */ |
---|
991 | if (!h5) |
---|
992 | return NC_ENOTNC4; |
---|
993 | |
---|
994 | /* Find var cause I need the number of dims. */ |
---|
995 | if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var))) |
---|
996 | return retval; |
---|
997 | |
---|
998 | /* Allocate space for the size_t copy of the chunksizes array. */ |
---|
999 | if (var->ndims) |
---|
1000 | if (!(cs = malloc(var->ndims * sizeof(size_t)))) |
---|
1001 | return NC_ENOMEM; |
---|
1002 | |
---|
1003 | retval = NC4_inq_var_all(ncid, varid, NULL, NULL, NULL, NULL, NULL, |
---|
1004 | NULL, NULL, NULL, NULL, contiguousp, cs, NULL, |
---|
1005 | NULL, NULL, NULL, NULL); |
---|
1006 | |
---|
1007 | /* Copy to size_t array. */ |
---|
1008 | if (*contiguousp == NC_CHUNKED) |
---|
1009 | for (i = 0; i < var->ndims; i++) |
---|
1010 | { |
---|
1011 | chunksizesp[i] = cs[i]; |
---|
1012 | if (cs[i] > NC_MAX_INT) |
---|
1013 | retval = NC_ERANGE; |
---|
1014 | } |
---|
1015 | |
---|
1016 | if (var->ndims) |
---|
1017 | free(cs); |
---|
1018 | return retval; |
---|
1019 | } |
---|
1020 | |
---|
1021 | /* This function defines the chunking with ints, which works better |
---|
1022 | * with F77 portability. It is a secret function, which has been |
---|
1023 | * rendered unmappable, and it is impossible to apparate anywhere in |
---|
1024 | * this function. */ |
---|
1025 | int |
---|
1026 | nc_def_var_chunking_ints(int ncid, int varid, int contiguous, int *chunksizesp) |
---|
1027 | { |
---|
1028 | NC_FILE_INFO_T *nc; |
---|
1029 | NC_GRP_INFO_T *grp; |
---|
1030 | NC_HDF5_FILE_INFO_T *h5; |
---|
1031 | NC_VAR_INFO_T *var; |
---|
1032 | size_t *cs = NULL; |
---|
1033 | int i, retval; |
---|
1034 | |
---|
1035 | /* Find this ncid's file info. */ |
---|
1036 | if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) |
---|
1037 | return retval; |
---|
1038 | assert(nc); |
---|
1039 | |
---|
1040 | /* Must be netcdf-4. */ |
---|
1041 | if (!h5) |
---|
1042 | return NC_ENOTNC4; |
---|
1043 | |
---|
1044 | /* Find var cause I need the number of dims. */ |
---|
1045 | if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var))) |
---|
1046 | return retval; |
---|
1047 | |
---|
1048 | /* Allocate space for the size_t copy of the chunksizes array. */ |
---|
1049 | if (var->ndims) |
---|
1050 | if (!(cs = malloc(var->ndims * sizeof(size_t)))) |
---|
1051 | return NC_ENOMEM; |
---|
1052 | |
---|
1053 | /* Copy to size_t array. */ |
---|
1054 | for (i = 0; i < var->ndims; i++) |
---|
1055 | cs[i] = chunksizesp[i]; |
---|
1056 | |
---|
1057 | retval = nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, |
---|
1058 | &contiguous, cs, NULL, NULL, NULL, NULL, NULL); |
---|
1059 | |
---|
1060 | if (var->ndims) |
---|
1061 | free(cs); |
---|
1062 | return retval; |
---|
1063 | } |
---|
1064 | |
---|
1065 | /* Define fill value behavior for a variable. This must be done after |
---|
1066 | nc_def_var and before nc_enddef. */ |
---|
1067 | int |
---|
1068 | NC4_def_var_fill(int ncid, int varid, int no_fill, const void *fill_value) |
---|
1069 | { |
---|
1070 | return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, NULL, |
---|
1071 | NULL, &no_fill, fill_value, NULL, NULL, NULL); |
---|
1072 | } |
---|
1073 | |
---|
1074 | |
---|
1075 | /* Define the endianness of a variable. */ |
---|
1076 | int |
---|
1077 | NC4_def_var_endian(int ncid, int varid, int endianness) |
---|
1078 | { |
---|
1079 | return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, NULL, |
---|
1080 | NULL, NULL, NULL, &endianness, NULL, NULL); |
---|
1081 | } |
---|
1082 | |
---|
1083 | /* Get var id from name. */ |
---|
1084 | int |
---|
1085 | NC4_inq_varid(int ncid, const char *name, int *varidp) |
---|
1086 | { |
---|
1087 | NC_FILE_INFO_T *nc; |
---|
1088 | NC_GRP_INFO_T *grp; |
---|
1089 | NC_HDF5_FILE_INFO_T *h5; |
---|
1090 | NC_VAR_INFO_T *var; |
---|
1091 | char norm_name[NC_MAX_NAME + 1]; |
---|
1092 | int retval; |
---|
1093 | |
---|
1094 | if (!name) |
---|
1095 | return NC_EINVAL; |
---|
1096 | if (!varidp) |
---|
1097 | return NC_NOERR; |
---|
1098 | |
---|
1099 | LOG((2, "nc_inq_varid: ncid 0x%x name %s", ncid, name)); |
---|
1100 | |
---|
1101 | /* Find info for this file and group, and set pointer to each. */ |
---|
1102 | if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) |
---|
1103 | return retval; |
---|
1104 | |
---|
1105 | /* Handle netcdf-3. */ |
---|
1106 | assert(h5); |
---|
1107 | |
---|
1108 | /* Normalize name. */ |
---|
1109 | if ((retval = nc4_normalize_name(name, norm_name))) |
---|
1110 | return retval; |
---|
1111 | |
---|
1112 | /* Find var of this name. */ |
---|
1113 | for (var = grp->var; var; var = var->next) |
---|
1114 | if (!(strcmp(var->name, norm_name))) |
---|
1115 | { |
---|
1116 | *varidp = var->varid; |
---|
1117 | return NC_NOERR; |
---|
1118 | } |
---|
1119 | |
---|
1120 | return NC_ENOTVAR; |
---|
1121 | } |
---|
1122 | |
---|
1123 | /* Rename a var to "bubba," for example. |
---|
1124 | |
---|
1125 | According to the netcdf-3.5 docs: If the new name is longer than |
---|
1126 | the old name, the netCDF dataset must be in define mode. */ |
---|
1127 | int |
---|
1128 | NC4_rename_var(int ncid, int varid, const char *name) |
---|
1129 | { |
---|
1130 | NC_FILE_INFO_T *nc; |
---|
1131 | NC_GRP_INFO_T *grp; |
---|
1132 | NC_HDF5_FILE_INFO_T *h5; |
---|
1133 | NC_VAR_INFO_T *var; |
---|
1134 | int retval = NC_NOERR; |
---|
1135 | |
---|
1136 | LOG((2, "nc_rename_var: ncid 0x%x varid %d name %s", |
---|
1137 | ncid, varid, name)); |
---|
1138 | |
---|
1139 | /* Find info for this file and group, and set pointer to each. */ |
---|
1140 | if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) |
---|
1141 | return retval; |
---|
1142 | |
---|
1143 | #ifdef USE_PNETCDF |
---|
1144 | /* Take care of files created/opened with parallel-netcdf library. */ |
---|
1145 | if (nc->pnetcdf_file) |
---|
1146 | return ncmpi_rename_var(nc->int_ncid, varid, name); |
---|
1147 | #endif /* USE_PNETCDF */ |
---|
1148 | |
---|
1149 | /* Take care of netcdf-3 files. */ |
---|
1150 | assert(h5); |
---|
1151 | |
---|
1152 | /* Is the new name too long? */ |
---|
1153 | if (strlen(name) > NC_MAX_NAME) |
---|
1154 | return NC_EMAXNAME; |
---|
1155 | |
---|
1156 | /* Trying to write to a read-only file? No way, Jose! */ |
---|
1157 | if (h5->no_write) |
---|
1158 | return NC_EPERM; |
---|
1159 | |
---|
1160 | /* Check name validity, if strict nc3 rules are in effect for this |
---|
1161 | * file. */ |
---|
1162 | if ((retval = NC_check_name(name))) |
---|
1163 | return retval; |
---|
1164 | |
---|
1165 | /* Is name in use? */ |
---|
1166 | for (var = grp->var; var; var = var->next) |
---|
1167 | if (!strncmp(var->name, name, NC_MAX_NAME)) |
---|
1168 | return NC_ENAMEINUSE; |
---|
1169 | |
---|
1170 | /* Find the var. */ |
---|
1171 | for (var = grp->var; var; var = var->next) |
---|
1172 | if (var->varid == varid) |
---|
1173 | break; |
---|
1174 | if (!var) |
---|
1175 | return NC_ENOTVAR; |
---|
1176 | |
---|
1177 | /* If we're not in define mode, new name must be of equal or |
---|
1178 | less size, if strict nc3 rules are in effect for this . */ |
---|
1179 | if (!(h5->flags & NC_INDEF) && strlen(name) > strlen(var->name) && |
---|
1180 | (h5->cmode & NC_CLASSIC_MODEL)) |
---|
1181 | return NC_ENOTINDEFINE; |
---|
1182 | |
---|
1183 | /* Change the HDF5 file, if this var has already been created |
---|
1184 | there. */ |
---|
1185 | if (var->created) |
---|
1186 | { |
---|
1187 | if (H5Gmove(grp->hdf_grpid, var->name, name) < 0) |
---|
1188 | BAIL(NC_EHDFERR); |
---|
1189 | } |
---|
1190 | |
---|
1191 | /* Now change the name in our metadata. */ |
---|
1192 | free(var->name); |
---|
1193 | if (!(var->name = malloc((strlen(name) + 1) * sizeof(char)))) |
---|
1194 | return NC_ENOMEM; |
---|
1195 | strcpy(var->name, name); |
---|
1196 | |
---|
1197 | exit: |
---|
1198 | return retval; |
---|
1199 | } |
---|
1200 | |
---|
1201 | |
---|
1202 | int |
---|
1203 | NC4_var_par_access(int ncid, int varid, int par_access) |
---|
1204 | { |
---|
1205 | #ifndef USE_PARALLEL |
---|
1206 | return NC_ENOPAR; |
---|
1207 | #else |
---|
1208 | NC_FILE_INFO_T *nc; |
---|
1209 | NC_GRP_INFO_T *grp; |
---|
1210 | NC_HDF5_FILE_INFO_T *h5; |
---|
1211 | NC_VAR_INFO_T *var; |
---|
1212 | int retval; |
---|
1213 | |
---|
1214 | LOG((1, "nc_var_par_access: ncid 0x%x varid %d par_access %d", ncid, |
---|
1215 | varid, par_access)); |
---|
1216 | |
---|
1217 | if (par_access != NC_INDEPENDENT && par_access != NC_COLLECTIVE) |
---|
1218 | return NC_EINVAL; |
---|
1219 | |
---|
1220 | /* Find info for this file and group, and set pointer to each. */ |
---|
1221 | if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) |
---|
1222 | return retval; |
---|
1223 | |
---|
1224 | #ifdef USE_PNETCDF |
---|
1225 | /* Handle files opened/created with parallel-netcdf library. */ |
---|
1226 | if (nc->pnetcdf_file) |
---|
1227 | { |
---|
1228 | if (par_access == nc->pnetcdf_access_mode) |
---|
1229 | return NC_NOERR; |
---|
1230 | |
---|
1231 | nc->pnetcdf_access_mode = par_access; |
---|
1232 | if (par_access == NC_INDEPENDENT) |
---|
1233 | return ncmpi_begin_indep_data(nc->int_ncid); |
---|
1234 | else |
---|
1235 | return ncmpi_end_indep_data(nc->int_ncid); |
---|
1236 | } |
---|
1237 | #endif /* USE_PNETCDF */ |
---|
1238 | |
---|
1239 | /* This function only for files opened with nc_open_par or nc_create_par. */ |
---|
1240 | if (!h5->parallel) |
---|
1241 | return NC_ENOPAR; |
---|
1242 | |
---|
1243 | /* Find the var, and set its preference. */ |
---|
1244 | for (var = grp->var; var; var = var->next) |
---|
1245 | if (var->varid == varid) |
---|
1246 | break; |
---|
1247 | if (!var) |
---|
1248 | return NC_ENOTVAR; |
---|
1249 | |
---|
1250 | if (par_access) |
---|
1251 | var->parallel_access = NC_COLLECTIVE; |
---|
1252 | else |
---|
1253 | var->parallel_access = NC_INDEPENDENT; |
---|
1254 | return NC_NOERR; |
---|
1255 | #endif /* USE_PARALLEL */ |
---|
1256 | } |
---|
1257 | |
---|
1258 | static int |
---|
1259 | nc4_put_vara_tc(int ncid, int varid, nc_type mem_type, int mem_type_is_long, |
---|
1260 | const size_t *startp, const size_t *countp, const void *op) |
---|
1261 | { |
---|
1262 | NC_FILE_INFO_T *nc; |
---|
1263 | |
---|
1264 | LOG((2, "nc4_put_vara_tc: ncid 0x%x varid %d mem_type %d mem_type_is_long %d", |
---|
1265 | ncid, varid, mem_type, mem_type_is_long)); |
---|
1266 | |
---|
1267 | if (!(nc = nc4_find_nc_file(ncid))) |
---|
1268 | return NC_EBADID; |
---|
1269 | |
---|
1270 | #ifdef USE_PNETCDF |
---|
1271 | /* Handle files opened/created with the parallel-netcdf library. */ |
---|
1272 | if (nc->pnetcdf_file) |
---|
1273 | { |
---|
1274 | MPI_Offset mpi_start[NC_MAX_DIMS], mpi_count[NC_MAX_DIMS]; |
---|
1275 | int d; |
---|
1276 | |
---|
1277 | /* No NC_LONGs for parallel-netcdf library! */ |
---|
1278 | if (mem_type_is_long) |
---|
1279 | return NC_EINVAL; |
---|
1280 | |
---|
1281 | /* We must convert the start, count, and stride arrays to |
---|
1282 | * MPI_Offset type. */ |
---|
1283 | for (d = 0; d < nc->pnetcdf_ndims[varid]; d++) |
---|
1284 | { |
---|
1285 | mpi_start[d] = startp[d]; |
---|
1286 | mpi_count[d] = countp[d]; |
---|
1287 | } |
---|
1288 | |
---|
1289 | if (nc->pnetcdf_access_mode == NC_INDEPENDENT) |
---|
1290 | { |
---|
1291 | switch(mem_type) |
---|
1292 | { |
---|
1293 | case NC_BYTE: |
---|
1294 | return ncmpi_put_vara_schar(nc->int_ncid, varid, mpi_start, mpi_count, op); |
---|
1295 | case NC_UBYTE: |
---|
1296 | return ncmpi_put_vara_uchar(nc->int_ncid, varid, mpi_start, mpi_count, op); |
---|
1297 | case NC_CHAR: |
---|
1298 | return ncmpi_put_vara_text(nc->int_ncid, varid, mpi_start, mpi_count, op); |
---|
1299 | case NC_SHORT: |
---|
1300 | return ncmpi_put_vara_short(nc->int_ncid, varid, mpi_start, mpi_count, op); |
---|
1301 | case NC_INT: |
---|
1302 | return ncmpi_put_vara_int(nc->int_ncid, varid, mpi_start, mpi_count, op); |
---|
1303 | case NC_FLOAT: |
---|
1304 | return ncmpi_put_vara_float(nc->int_ncid, varid, mpi_start, mpi_count, op); |
---|
1305 | case NC_DOUBLE: |
---|
1306 | return ncmpi_put_vara_double(nc->int_ncid, varid, mpi_start, mpi_count, op); |
---|
1307 | case NC_NAT: |
---|
1308 | default: |
---|
1309 | return NC_EBADTYPE; |
---|
1310 | } |
---|
1311 | } |
---|
1312 | else |
---|
1313 | { |
---|
1314 | switch(mem_type) |
---|
1315 | { |
---|
1316 | case NC_BYTE: |
---|
1317 | return ncmpi_put_vara_schar_all(nc->int_ncid, varid, mpi_start, mpi_count, op); |
---|
1318 | case NC_UBYTE: |
---|
1319 | return ncmpi_put_vara_uchar_all(nc->int_ncid, varid, mpi_start, mpi_count, op); |
---|
1320 | case NC_CHAR: |
---|
1321 | return ncmpi_put_vara_text_all(nc->int_ncid, varid, mpi_start, mpi_count, op); |
---|
1322 | case NC_SHORT: |
---|
1323 | return ncmpi_put_vara_short_all(nc->int_ncid, varid, mpi_start, mpi_count, op); |
---|
1324 | case NC_INT: |
---|
1325 | return ncmpi_put_vara_int_all(nc->int_ncid, varid, mpi_start, mpi_count, op); |
---|
1326 | case NC_FLOAT: |
---|
1327 | return ncmpi_put_vara_float_all(nc->int_ncid, varid, mpi_start, mpi_count, op); |
---|
1328 | case NC_DOUBLE: |
---|
1329 | return ncmpi_put_vara_double_all(nc->int_ncid, varid, mpi_start, mpi_count, op); |
---|
1330 | case NC_NAT: |
---|
1331 | default: |
---|
1332 | return NC_EBADTYPE; |
---|
1333 | } |
---|
1334 | } |
---|
1335 | } |
---|
1336 | #endif /* USE_PNETCDF */ |
---|
1337 | |
---|
1338 | /* NetCDF-3 cases handled by dispatch layer. */ |
---|
1339 | assert(nc->nc4_info); |
---|
1340 | |
---|
1341 | return nc4_put_vara(nc, ncid, varid, startp, countp, mem_type, |
---|
1342 | mem_type_is_long, (void *)op); |
---|
1343 | } |
---|
1344 | |
---|
1345 | int |
---|
1346 | nc4_get_hdf4_vara(NC_FILE_INFO_T *nc, int ncid, int varid, const size_t *startp, |
---|
1347 | const size_t *countp, nc_type mem_nc_type, int is_long, void *data) |
---|
1348 | { |
---|
1349 | #ifdef USE_HDF4 |
---|
1350 | NC_GRP_INFO_T *grp, *g; |
---|
1351 | NC_HDF5_FILE_INFO_T *h5; |
---|
1352 | NC_VAR_INFO_T *var; |
---|
1353 | NC_DIM_INFO_T *dim; |
---|
1354 | int32 start32[NC_MAX_VAR_DIMS], edge32[NC_MAX_VAR_DIMS]; |
---|
1355 | int retval, d; |
---|
1356 | |
---|
1357 | /* Find our metadata for this file, group, and var. */ |
---|
1358 | assert(nc); |
---|
1359 | if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var))) |
---|
1360 | return retval; |
---|
1361 | h5 = nc->nc4_info; |
---|
1362 | assert(grp && h5 && var && var->name); |
---|
1363 | |
---|
1364 | for (d = 0; d < var->ndims; d++) |
---|
1365 | { |
---|
1366 | start32[d] = startp[d]; |
---|
1367 | edge32[d] = countp[d]; |
---|
1368 | } |
---|
1369 | |
---|
1370 | if (SDreaddata(var->sdsid, start32, NULL, edge32, data)) |
---|
1371 | return NC_EHDFERR; |
---|
1372 | |
---|
1373 | #endif /* USE_HDF4 */ |
---|
1374 | return NC_NOERR; |
---|
1375 | } |
---|
1376 | |
---|
1377 | /* Get an array. */ |
---|
1378 | static int |
---|
1379 | nc4_get_vara_tc(int ncid, int varid, nc_type mem_type, int mem_type_is_long, |
---|
1380 | const size_t *startp, const size_t *countp, void *ip) |
---|
1381 | { |
---|
1382 | NC_FILE_INFO_T *nc; |
---|
1383 | |
---|
1384 | LOG((2, "nc4_get_vara_tc: ncid 0x%x varid %d mem_type %d mem_type_is_long %d", |
---|
1385 | ncid, varid, mem_type, mem_type_is_long)); |
---|
1386 | |
---|
1387 | if (!(nc = nc4_find_nc_file(ncid))) |
---|
1388 | return NC_EBADID; |
---|
1389 | |
---|
1390 | #ifdef USE_PNETCDF |
---|
1391 | /* Handle files opened/created with the parallel-netcdf library. */ |
---|
1392 | if (nc->pnetcdf_file) |
---|
1393 | { |
---|
1394 | MPI_Offset mpi_start[NC_MAX_VAR_DIMS], mpi_count[NC_MAX_VAR_DIMS]; |
---|
1395 | int d; |
---|
1396 | |
---|
1397 | /* No NC_LONGs for parallel-netcdf library! */ |
---|
1398 | if (mem_type_is_long) |
---|
1399 | return NC_EINVAL; |
---|
1400 | |
---|
1401 | /* We must convert the start, count, and stride arrays to |
---|
1402 | * MPI_Offset type. */ |
---|
1403 | for (d = 0; d < nc->pnetcdf_ndims[varid]; d++) |
---|
1404 | { |
---|
1405 | mpi_start[d] = startp[d]; |
---|
1406 | mpi_count[d] = countp[d]; |
---|
1407 | } |
---|
1408 | |
---|
1409 | if (nc->pnetcdf_access_mode == NC_INDEPENDENT) |
---|
1410 | { |
---|
1411 | switch(mem_type) |
---|
1412 | { |
---|
1413 | case NC_BYTE: |
---|
1414 | return ncmpi_get_vara_schar(nc->int_ncid, varid, mpi_start, mpi_count, ip); |
---|
1415 | case NC_UBYTE: |
---|
1416 | return ncmpi_get_vara_uchar(nc->int_ncid, varid, mpi_start, mpi_count, ip); |
---|
1417 | case NC_CHAR: |
---|
1418 | return ncmpi_get_vara_text(nc->int_ncid, varid, mpi_start, mpi_count, ip); |
---|
1419 | case NC_SHORT: |
---|
1420 | return ncmpi_get_vara_short(nc->int_ncid, varid, mpi_start, mpi_count, ip); |
---|
1421 | case NC_INT: |
---|
1422 | return ncmpi_get_vara_int(nc->int_ncid, varid, mpi_start, mpi_count, ip); |
---|
1423 | case NC_FLOAT: |
---|
1424 | return ncmpi_get_vara_float(nc->int_ncid, varid, mpi_start, mpi_count, ip); |
---|
1425 | case NC_DOUBLE: |
---|
1426 | return ncmpi_get_vara_double(nc->int_ncid, varid, mpi_start, mpi_count, ip); |
---|
1427 | case NC_NAT: |
---|
1428 | default: |
---|
1429 | return NC_EBADTYPE; |
---|
1430 | } |
---|
1431 | } |
---|
1432 | else |
---|
1433 | { |
---|
1434 | switch(mem_type) |
---|
1435 | { |
---|
1436 | case NC_BYTE: |
---|
1437 | return ncmpi_get_vara_schar_all(nc->int_ncid, varid, mpi_start, mpi_count, ip); |
---|
1438 | case NC_UBYTE: |
---|
1439 | return ncmpi_get_vara_uchar_all(nc->int_ncid, varid, mpi_start, mpi_count, ip); |
---|
1440 | case NC_CHAR: |
---|
1441 | return ncmpi_get_vara_text_all(nc->int_ncid, varid, mpi_start, mpi_count, ip); |
---|
1442 | case NC_SHORT: |
---|
1443 | return ncmpi_get_vara_short_all(nc->int_ncid, varid, mpi_start, mpi_count, ip); |
---|
1444 | case NC_INT: |
---|
1445 | return ncmpi_get_vara_int_all(nc->int_ncid, varid, mpi_start, mpi_count, ip); |
---|
1446 | case NC_FLOAT: |
---|
1447 | return ncmpi_get_vara_float_all(nc->int_ncid, varid, mpi_start, mpi_count, ip); |
---|
1448 | case NC_DOUBLE: |
---|
1449 | return ncmpi_get_vara_double_all(nc->int_ncid, varid, mpi_start, mpi_count, ip); |
---|
1450 | case NC_NAT: |
---|
1451 | default: |
---|
1452 | return NC_EBADTYPE; |
---|
1453 | } |
---|
1454 | } |
---|
1455 | } |
---|
1456 | #endif /* USE_PNETCDF */ |
---|
1457 | |
---|
1458 | /* Handle netCDF-3 cases. */ |
---|
1459 | assert(nc->nc4_info); |
---|
1460 | |
---|
1461 | /* Handle HDF4 cases. */ |
---|
1462 | if (nc->nc4_info->hdf4) |
---|
1463 | return nc4_get_hdf4_vara(nc, ncid, varid, startp, countp, mem_type, |
---|
1464 | mem_type_is_long, (void *)ip); |
---|
1465 | |
---|
1466 | /* Handle HDF5 cases. */ |
---|
1467 | return nc4_get_vara(nc, ncid, varid, startp, countp, mem_type, |
---|
1468 | mem_type_is_long, (void *)ip); |
---|
1469 | } |
---|
1470 | |
---|
1471 | int |
---|
1472 | NC4_put_vara(int ncid, int varid, const size_t *startp, |
---|
1473 | const size_t *countp, const void *op, int memtype) |
---|
1474 | { |
---|
1475 | return nc4_put_vara_tc(ncid, varid, memtype, 0, startp, countp, op); |
---|
1476 | } |
---|
1477 | |
---|
1478 | |
---|
1479 | /* Read an array of values. */ |
---|
1480 | int |
---|
1481 | NC4_get_vara(int ncid, int varid, const size_t *startp, |
---|
1482 | const size_t *countp, void *ip, int memtype) |
---|
1483 | { |
---|
1484 | return nc4_get_vara_tc(ncid, varid, memtype, 0, startp, countp, ip); |
---|
1485 | } |
---|