Changeset 494


Ignore:
Timestamp:
Mar 1, 2010 12:23:32 PM (12 years ago)
Author:
raasch
Message:

last commit documented; configuration example file for netcdf4 added

Location:
palm/trunk
Files:
1 added
16 edited

Legend:

Unmodified
Added
Removed
  • palm/trunk/DOC/tec/technical_documentation.html

    r493 r494  
    11<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
    22<html><head>
     3
    34
    45
     
    7879   
    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>
     126combine_plot_fields<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>
     171trunk/UTIL/Makefile<br>
     172      </td>
     173    </tr>
     174<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>
  • palm/trunk/SCRIPTS/.mrun.config.imuk_hlrn

    r346 r494  
    4646#
    4747%sgi_feature       ice                                        lcsgih parallel
     48%modules           ifort/11.0.069:mvapich2/1.4.0-intel:netcdf lcsgih parallel
    4849#%remote_username  <replace by your HLRN username>            lcsgih parallel
    4950%compiler_name     mpif90                                     lcsgih parallel
    5051%compiler_name_ser ifort                                      lcsgih parallel
    51 %mpilib            mvapich2/1.2.0-intel                       lcsgih parallel
    52 %cpp_options       -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit   lcsgih parallel
     52%cpp_options       -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf   lcsgih parallel
    5353%netcdf_inc        -I:/sw/dataformats/netcdf/3.6.2/include    lcsgih parallel
    5454%netcdf_lib        -L/sw/dataformats/netcdf/3.6.2/lib:-lnetcdf:-lnetcdff      lcsgih parallel
  • palm/trunk/SOURCE/check_open.f90

    r493 r494  
    44! Current revisions:
    55! -----------------
    6 ! NetCDF4 support (parallel output)
     6!
    77!
    88! Former revisions:
    99! -----------------
    1010! $Id$
     11!
     12! 493 2010-03-01 08:30:24Z raasch
     13! NetCDF4 support (parallel output)
    1114!
    1215! 410 2009-12-04 17:05:40Z letzel
  • palm/trunk/SOURCE/check_parameters.f90

    r493 r494  
    44! Current revisions:
    55! -----------------
    6 ! netcdf_data_format is checked
     6!
    77!
    88! Former revisions:
    99! -----------------
    1010! $Id$
     11!
     12! 493 2010-03-01 08:30:24Z raasch
     13! netcdf_data_format is checked
    1114!
    1215! 411 2009-12-11 14:15:58Z heinze
  • palm/trunk/SOURCE/close_file.f90

    r493 r494  
    44! Current revisions:
    55! -----------------
    6 ! Adjustments for NetCDF parallel data output
     6!
    77!
    88! Former revisions:
    99! -----------------
    1010! $Id$
     11!
     12! 493 2010-03-01 08:30:24Z raasch
     13! Adjustments for NetCDF parallel data output
    1114!
    1215! 410 2009-12-04 17:05:40Z letzel
  • palm/trunk/SOURCE/data_output_2d.f90

    r493 r494  
    99! -----------------
    1010! $Id$
     11!
     12! 493 2010-03-01 08:30:24Z raasch
     13! NetCDF4 support (parallel output)
    1114!
    1215! 367 2009-08-25 08:35:52Z maronga
  • palm/trunk/SOURCE/data_output_3d.f90

    r493 r494  
    99! -----------------
    1010! $Id$
     11!
     12! 493 2010-03-01 08:30:24Z raasch
     13! NetCDF4 support (parallel output)
    1114!
    1215! 355 2009-07-17 01:03:01Z letzel
  • palm/trunk/SOURCE/data_output_mask.f90

    r493 r494  
    99! -----------------
    1010! $Id$
     11!
     12! 493 2010-03-01 08:30:24Z raasch
     13! netcdf_format_mask* and format_parallel_io replaced by netcdf_data_format
    1114!
    1215! 475 2010-02-04 02:26:16Z raasch
  • palm/trunk/SOURCE/header.f90

    r493 r494  
    44! Current revisions:
    55! -----------------
    6 ! NetCDF data output format extendend for NetCDF4/HDF5
     6!
    77!
    88! Former revisions:
    99! -----------------
    1010! $Id$
     11!
     12! 493 2010-03-01 08:30:24Z raasch
     13! NetCDF data output format extendend for NetCDF4/HDF5
    1114!
    1215! 449 2010-02-02 11:23:59Z raasch
  • palm/trunk/SOURCE/init_masks.f90

    r493 r494  
    99! -----------------
    1010! $Id$
     11!
     12! 493 2010-03-01 08:30:24Z raasch
     13! netcdf_format_mask* and format_parallel_io replaced by netcdf_data_format
    1114!
    1215! 410 2009-12-04 17:05:40Z letzel
  • palm/trunk/SOURCE/modules.f90

    r493 r494  
    55! Current revisions:
    66! -----------------
    7 ! +netcdf_data_format, -netcdf_64bit, -netcdf_64bit_3d
     7!
    88!
    99! Former revisions:
    1010! -----------------
    1111! $Id$
     12!
     13! 493 2010-03-01 08:30:24Z raasch
     14! +netcdf_data_format, -netcdf_64bit, -netcdf_64bit_3d, -netcdf_format_mask*,
     15! -nc_format_mask, -format_parallel_io
    1216!
    1317! 485 2010-02-05 10:57:51Z raasch
  • palm/trunk/SOURCE/netcdf.f90

    r493 r494  
    77! Current revisions:
    88! ------------------
    9 ! Extensions for NetCDF4 output
     9!
    1010!
    1111! Former revisions:
    1212! -----------------
    1313! $Id$
     14!
     15! 493 2010-03-01 08:30:24Z raasch
     16! Extensions for NetCDF4 output
    1417!
    1518! 410 2009-12-04 17:05:40Z letzel
  • palm/trunk/SOURCE/parin.f90

    r493 r494  
    44! Current revisions:
    55! -----------------
    6 ! +netcdf_data_format in d3par, -netcdf_64bit, -netcdf_64bit_3d
     6!
    77!
    88! Former revisions:
    99! -----------------
    1010! $Id$
     11!
     12! 493 2010-03-01 08:30:24Z raasch
     13! +netcdf_data_format in d3par, -netcdf_64bit, -netcdf_64bit_3d
    1114!
    1215! 449 2010-02-02 11:23:59Z raasch
  • palm/trunk/SOURCE/user_statistics.f90

    r493 r494  
    44! Current revisions:
    55! -----------------
    6 ! Bugfix: timeseries data have to be collected by PE0
     6!
    77!
    88! Former revisions:
    99! -----------------
    1010! $Id$
     11!
     12! 493 2010-03-01 08:30:24Z raasch
     13! Bugfix: timeseries data have to be collected by PE0
    1114!
    1215! 211 2008-11-11 04:46:24Z raasch
  • palm/trunk/UTIL/Makefile

    • Property svn:keywords set to Id
  • palm/trunk/UTIL/combine_plot_fields.f90

    r493 r494  
    44! Actual revisions:
    55! -----------------
    6 ! Exit in case of already complete NetCDF data (due to parallel output in PALM)
    7 ! cpu measurements included
     6!
    87!
    98! Former revisions:
    109! -----------------
    1110! $Id$
     11!
     12! 493 2010-03-01 08:30:24Z raasch
     13! Exit in case of already complete NetCDF data (due to parallel output in PALM)
     14! cpu measurements included
    1215!
    1316! 210 2008-11-06 08:54:02Z raasch
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