Changeset 494 for palm/trunk/DOC/tec/technical_documentation.html
- Timestamp:
- Mar 1, 2010 12:23:32 PM (14 years ago)
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palm/trunk/DOC/tec/technical_documentation.html (modified) (4 diffs)
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palm/trunk/DOC/tec/technical_documentation.html
r493 r494 1 1 <!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en"> 2 2 <html><head> 3 3 4 4 5 … … 78 79 79 80 <tr> 81 <td style="vertical-align: top;">01/03/10<br> 82 </td> 83 <td style="vertical-align: top;">SR<br> 84 </td> 85 <td style="vertical-align: top;">494<br> 86 </td> 87 <td style="vertical-align: top;">3.7a<br> 88 </td> 89 <td style="vertical-align: top;">N<br> 90 </td> 91 <td style="vertical-align: top;">Output in NetCDF4-format.<br> 92 <br> 93 NetCDF4 allows for parallel I/O. Also, variables are not limited in 94 size any more (i.e. arrays can be larger than 2GB). The new 95 d3par-parameter <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span>.can be used to select among the different NetCDF file formats (<span style="font-style: italic;">1</span>: classic format, <span style="font-style: italic;">2</span>: 64-bit-offset format (this is now the default), <span style="font-style: italic;">3</span>: NetCDF4/HDF5 format, <span style="font-style: italic;">4</span>: NetCDF4 format with NF90_CLASSIC_MODEL bit set). Setting <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span> > <span style="font-style: italic;">2</span> 96 only affects 2d- and 3d-output, i.e. there is no parallel output for 97 profiles, time series, spectra, and particles. Parallel output of 98 particle data may realized in the future.<br> 99 <br> 100 In case of parallel output, all PEs write into one file, which means that postprocessing the data with <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> 101 (merging data from single files - one per PE - into one file) is not 102 neccessary. In this case, flag files are automatically set, telling <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> that nothing is to be done.<br> 103 <br> 104 Using NetCDF4 format requires a NetCDF4/HDF library. Respective 105 settings for -I, -L, and -l compiler/loader options for the SGI-ICE at 106 HLRN can be found in the new example configuration file <span style="font-family: Courier New,Courier,monospace;">..../trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4</span><br> 107 <br> 108 <span style="font-weight: bold;">Attention:</span><br> 109 So far, NetCDF parallel I/O has only been tested a little. Further 110 performance optimizations may be required, especially in case of large 111 data sets (e.g. data chunking, or lustre file system settings with <span style="font-family: Courier New,Courier,monospace;">lfs setstripe</span>). <span style="font-weight: bold;">Please report bugs and performance problems immediately!</span><br> 112 <br> 113 <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br> 114 <br> 115 Modules to be loaded for compilation (mbuild) or job execution (mrun) can/should now be given in the configuration file (<span style="font-family: Courier New,Courier,monospace;">.mrun.config</span>) using variable <span style="font-family: Courier New,Courier,monospace;">modules</span>. Example:<br> 116 <br> 117 <span style="font-family: Courier New,Courier,monospace;"> %modules ifort/11.0.069:netcdf lcsgih parallel</span><br> 118 <br> 119 This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br> 120 <br> 121 <span style="font-weight: bold;">WARNING:</span><br> 122 <span style="font-weight: bold;">All fixed settings of modules in the scripts mbuild, mrun, and subjob have been removed! Please set the <span style="font-family: Courier New,Courier,monospace;">modules</span> variable appropriately and remove the mpilib variable in your configuration file.</span><br> 123 </td> 124 <td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br> 125 <br> 126 combine_plot_fields<br> 127 <br> 128 mbuild, mrun, subjob<br> 129 </td> 130 </tr> 131 <tr> 132 <td style="vertical-align: top;"><br> 133 </td> 134 <td style="vertical-align: top;"><br> 135 </td> 136 <td style="vertical-align: top;"><br> 137 </td> 138 <td style="vertical-align: top;"><br> 139 </td> 140 <td style="vertical-align: top;">C<br> 141 </td> 142 <td style="vertical-align: top;">d3par-parameters <span style="font-family: Courier New,Courier,monospace;">netcdf_64bit</span> and <span style="font-family: Courier New,Courier,monospace;">netcdf_64bit_3d</span> have been removed. Use the new d3par-variable <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span> = <span style="font-style: italic;">2</span> 143 for choosing the NetCDF 64bit-offset format (this is the default from 144 now on). The offset-format can not be set independently for the 145 3d-output-data any more.<br> 146 <br> 147 d3par-parameters <span style="font-family: Courier New,Courier,monospace;">netcdf_format_mask</span>, <span style="font-family: Courier New,Courier,monospace;">netcdf_format_mask_av</span>, and variables <span style="font-family: Courier New,Courier,monospace;">nc_format_mask</span>, <span style="font-family: Courier New,Courier,monospace;">format_parallel_io</span> removed. They are replaced by the new parameter <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span>. This change concerns the masked data output, which is still not documented.<br> 148 </td> 149 <td style="vertical-align: top;">check_open, close_file,<br> 150 data_output_mask, header, init_masks, modules, parin<br> 151 <br> 152 </td> 153 </tr> 154 <tr> 155 <td style="vertical-align: top;"><br> 156 </td> 157 <td style="vertical-align: top;"><br> 158 </td> 159 <td style="vertical-align: top;"><br> 160 </td> 161 <td style="vertical-align: top;"><br> 162 </td> 163 <td style="vertical-align: top;">B<br> 164 </td> 165 <td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br> 166 <br> 167 Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br> 168 </td> 169 <td style="vertical-align: top;">user_statistics<br> 170 <br> 171 trunk/UTIL/Makefile<br> 172 </td> 173 </tr> 174 <tr> 80 175 <td style="vertical-align: top;">05/02/10<br> 81 176 </td> … … 84 179 <td style="vertical-align: top;">485<br> 85 180 </td> 86 <td style="vertical-align: top;"> <br>87 </td> 88 <td style="vertical-align: top;"> <br>181 <td style="vertical-align: top;">3.7a<br> 182 </td> 183 <td style="vertical-align: top;">B<br> 89 184 </td> 90 185 <td style="vertical-align: top;"><span style="font-family: Courier New,Courier,monospace;">ngp_3d</span>, <span style="font-family: Courier New,Courier,monospace;">ngp_3d_inner</span> … … 102 197 <td style="vertical-align: top;">484<br> 103 198 </td> 104 <td style="vertical-align: top;"> <br>199 <td style="vertical-align: top;">3.7a<br> 105 200 </td> 106 201 <td style="vertical-align: top;">B<br>
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