Changeset 494 for palm/trunk/DOC/tec

Mar 1, 2010 12:23:32 PM (14 years ago)

last commit documented; configuration example file for netcdf4 added

1 edited


  • palm/trunk/DOC/tec/technical_documentation.html

    r493 r494  
    11<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
    7980    <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>
     93NetCDF4 allows for parallel I/O. Also, variables are not limited in
     94size any more (i.e. arrays can be larger than 2GB). The new
     95d3par-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> &gt; <span style="font-style: italic;">2</span>
     96only affects 2d- and 3d-output, i.e. there is no parallel output for
     97profiles, time series, spectra, and particles. Parallel output of
     98particle data may realized in the future.<br>
     99      <br>
     100In 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
     102neccessary. 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>
     104Using NetCDF4 format requires a NetCDF4/HDF library. Respective
     105settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
     106HLRN 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>
     109So far, NetCDF parallel I/O has only been tested a little. Further
     110performance optimizations may be required, especially in case of large
     111data 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>
     115Modules 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;">&nbsp;&nbsp; %modules&nbsp;&nbsp;&nbsp;&nbsp; ifort/11.0.069:netcdf&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; lcsgih parallel</span><br>
     118      <br>
     119This 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>
     127      <br>
     128mbuild, 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>
     143for choosing the NetCDF 64bit-offset format (this is the default from
     144now on). The offset-format can not be set independently for the
     1453d-output-data any more.<br>
     146      <br>
     147d3par-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>
     150data_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>
     167Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
     168      </td>
     169      <td style="vertical-align: top;">user_statistics<br>
     170      <br>
     172      </td>
     173    </tr>
    80175      <td style="vertical-align: top;">05/02/10<br>
    81176      </td>
    84179      <td style="vertical-align: top;">485<br>
    85180      </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>
    89184      </td>
    90185      <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>
    102197      <td style="vertical-align: top;">484<br>
    103198      </td>
    104       <td style="vertical-align: top;"><br>
     199      <td style="vertical-align: top;">3.7a<br>
    105200      </td>
    106201      <td style="vertical-align: top;">B<br>
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