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Ignore:
Timestamp:
Mar 1, 2010 8:30:24 AM (14 years ago)
Author:
raasch
Message:

New:
---
Output in NetCDF4-format. New d3par-parameter netcdf_data_format.

(check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin)

Modules to be loaded for compilation (mbuild) or job execution (mrun)
can be given in the configuration file using variable modules. Example:

%modules ifort/11.0.069:netcdf lcsgih parallel

This method replaces the (undocumented) mpilib-variable.

WARNING: All fixed settings of modules in the scripts mbuild, mrun, and subjob
have been removed! Please set the modules variable appropriately in your
configuration file. (mbuild, mrun, subjob)

Changed:

Parameters netcdf_64bit and netcdf_64bit_3d have been removed. Use
netcdf_data_format = 2 for choosing the classic 64bit-offset format (this is
the default). The offset-format can not be set independently for the
3d-output-data any more.

Parameters netcdf_format_mask, netcdf_format_mask_av, and variables
nc_format_mask, format_parallel_io removed. They are replaced by the new
parameter netcdf_data_format. (check_open, close_file,
data_output_mask, header, init_masks, modules, parin)

Errors:

bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config

Bugfix: timeseries data have to be collected by PE0 (user_statistics)

File:
1 edited

Legend:

Unmodified
Added
Removed

  • palm/trunk/DOC/app/chapter_4.5.1.html

    r97 r493  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
    22<html><head>
     3
    34<meta content="text/html; charset=windows-1252" http-equiv="CONTENT-TYPE"><title>PALM chapter 4.5.1</title>
    45<meta content="StarOffice 7 (Win32)" name="GENERATOR">
    … …  
    78@page { size: 21cm 29.7cm }
    89-->
    9 </style></head>
    10 <body style="direction: ltr;" lang="en-US"><h4 style="line-height: 100%;"><font size="4">4.5.1
     10</style></head><body style="direction: ltr;" lang="en-US"><h4 style="line-height: 100%;"><font size="4">4.5.1
    1111NetCDF data output&nbsp;<span style="color: rgb(255, 0, 0);"></span></font></h4>
    1212<p style="line-height: 100%;">The standard data output of
    1313PALM is NetCDF (<span style="font-weight: bold;">Net</span>work
    14 <span style="font-weight: bold;">C</span>ommon <span style="font-weight: bold;">D</span>ata <span style="font-weight: bold;">F</span>orm). NetCDF is an
    15 interface to a library of data access functions<br>for
     14<span style="font-weight: bold;">C</span>ommon <span style="font-weight: bold;">D</span>ata <span style="font-weight: bold;">F</span>orm) in 64-bit offset format. NetCDF is an
     15interface to a library of data access functions for
    1616storing and retrieving data in the form of arrays. NetCDF is an
    1717abstraction that supports a view of data as a collection of
    … …  
    3636on <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/manual/netcdf/netcdf-3_f90_tutorial.pdf">our
    3737web server</a>.</p><p style="line-height: 100%;">The
    38 output format of PALM data is determined by the runtime-parameter <a href="chapter_4.2.html#data_output_format">data_output_format</a>
     38general output format of PALM data is determined by the runtime-parameter <a href="chapter_4.2.html#data_output_format">data_output_format</a>
    3939(<span style="font-weight: bold;">data_output_format</span>
    4040= <span style="font-style: italic;">'netcdf'</span>,
    … …  
    4242selected (see <a href="chapter_4.2.html#data_output_format">data_output_format</a>).
    4343The accuracy of the NetCDF output data can be set with parameter <a href="chapter_4.1.html#netcdf_precision">netcdf_precision</a>.
    44 By default, data have single (4 byte) precision. Also by default,
    45 NetCDF datasets (files) are not allowed to be larger than 2 GByte.
    46 Larger datasets can be created&nbsp;by setting <a href="chapter_4.2.html#netcdf_64bit">netcdf_64bit</a>
    47 = <span style="font-style: italic;">.TRUE.</span>.
    48 These files then have the so-called 64bit-offset format. However,
    49 currently, many of the existing application programs may not support
    50 this 64-bit offset format.<br></p>PALM allows the output of
     44By default, data have single (4 byte) precision. Runtime-parameter <a href="chapter_4.2.html#netcdf_data_format">netcdf_data_format</a>
     45can be used to choose between the different NetCDF file formats
     46(classic, 64-bit offset, NetCDF4/HDF5). The 64-bit offset format allows
     47creating large files (file size only limited by the underlying file
     48system), but each output variable (array) is still limited to 2GB. In
     49NetCDF4 format, there is no limit for the size of variables, and it
     50also allows parallel I/O into one output file. However, some (graphic)
     51software still does not support NetCDF4 format.<br></p>PALM allows the output of
    5152various
    5253data (e.g. cross sections, vertical profiles, timeseries, etc.) into
    … …  
    157158or <a href="chapter_4.2.html#skip_time_do3d">skip_time_do3d</a>)</td></tr><tr><td align="undefined" valign="undefined">particle
    158159timeseries</td><td style="vertical-align: top;"><a href="chapter_3.4.html#DATA_1D_PTS_NETCDF">DATA_1D_PTS_NETCDF</a></td><td style="vertical-align: top;"><a href="chapter_4.2.html#dt_data_output">dt_data_output</a>
    159 (or <a href="chapter_4.2.html#dt_dopts">dt_dopts</a>)</td><td align="undefined" valign="undefined"></td></tr><tr><td align="left" valign="top">particle attributes</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_PRT_NETCDF">DATA_PRT_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#dt_write_particle_data">dt_write_particle_data</a></td><td align="left" valign="top"></td></tr></tbody></table><br><br><span style="font-weight: bold;">Creating, contents and
     160(or <a href="chapter_4.2.html#dt_dopts">dt_dopts</a>)</td><td align="undefined" valign="undefined"><br>
     161</td></tr><tr><td align="left" valign="top">particle attributes</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_PRT_NETCDF">DATA_PRT_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#dt_write_particle_data">dt_write_particle_data</a></td><td align="left" valign="top"><br>
     162</td></tr></tbody></table><br><br><span style="font-weight: bold;">Creating, contents and
    160163post-processing of a PALM NetCDF file</span><br><br>This
    161164section describes, step-by-step, the creation, storage, and
    … …  
    208211the respective <b>mrun</b> call is
    209212like<br><br><span style="font-family: monospace;">&nbsp;
    210 &nbsp;mrun -d&nbsp; test -r &ldquo;xy#&rdquo; ... </span><br style="font-family: monospace;"><br>then the local
     213&nbsp;mrun -d&nbsp; test -r “xy#” ... </span><br style="font-family: monospace;"><br>then the local
    211214file <tt><font style="font-size: 10pt;" size="2">DATA_2D_XY_NETCDF</font></tt>
    212215is copied to the permanent file <tt><font style="font-size: 10pt;" size="2">~/test/OUTPUT/test/test_xy.nc</font>
    … …  
    229232which requires an additional file connection statement<br><br><span style="font-family: monospace;">&nbsp;&nbsp;
    230233DATA_2D_XY_AV_NETCDF out:loc:tr&nbsp; xy#&nbsp;
    231 ~/$fname/OUTPUT/$fname&nbsp; _xy_av nc&nbsp;&nbsp; .</span><br></p></li><li>With
     234~/$fname/OUTPUT/$fname&nbsp; _xy_av nc&nbsp;&nbsp; .</span><br></p></li><li>Using <a href="chapter_4.2.html#netcdf_data_format">netcdf_data_format</a> &gt; <span style="font-style: italic;">2</span> or <a href="chapter_4.2.html#data_output_2d_on_each_pe">data_output_2d_on_each_pe</a> = <span style="font-style: italic;">.F.</span> generates a single NetCDF file containing data from all propcessors. However, with
    232235parallel runs and choice of <a href="chapter_4.2.html#data_output_2d_on_each_pe">data_output_2d_on_each_pe</a>
    233236= <i>.T.</i>
    … …  
    293296example program.<br><br><br></li><li>By
    294297default, each PALM job creates its own NetCDF files. If permanent files
    295 with respective filenames are already existing then new files with
     298with respective filenames are already existing, then new files with
    296299higher cycle numbers will be created. However, in case of a job chain,
    297300it is possible to extend the NetCDF datasets created by the initial
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