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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

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    23 </head>
    24 
    25 
    26 <body>
     14  <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"><title>PALM chapter 4.2</title></head><body>
    2715
    2816
    … …  
    17331721     
    17341722      <p>Umlauts
    1735 are possible (write &ldquo; in front of, similar to TeX), as
     1723are possible (write &#8220; in front of, similar to TeX), as
    17361724well as super- and subscripts (use "&gt;" or "&lt;" in front of
    17371725each
    … …  
    20071995
    20081996
    2009             <td></td>
     1997            <td><br>
     1998</td>
    20101999
    20112000
    … …  
    20712060
    20722061
    2073             <td style="vertical-align: top;"></td>
     2062            <td style="vertical-align: top;"><br>
     2063</td>
    20742064
    20752065
    … …  
    22372227
    22382228
    2239             <td style="vertical-align: top;"></td>
     2229            <td style="vertical-align: top;"><br>
     2230</td>
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    … …  
    23912382
    23922383
    2393             <td style="vertical-align: top;"></td>
     2384            <td style="vertical-align: top;"><br>
     2385</td>
    23942386
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    … …  
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    26112603
    2612             <td style="vertical-align: top;"></td>
     2604            <td style="vertical-align: top;"><br>
     2605</td>
    26132606
    26142607
    … …  
    26732666
    26742667
    2675             <td style="vertical-align: top;"></td>
     2668            <td style="vertical-align: top;"><br>
     2669</td>
    26762670
    26772671
    … …  
    27352729
    27362730
    2737             <td style="vertical-align: top;"></td>
     2731            <td style="vertical-align: top;"><br>
     2732</td>
    27382733
    27392734
    … …  
    27652760
    27662761
    2767             <td></td>
     2762            <td><br>
     2763</td>
    27682764
    27692765
    … …  
    31093105the file
    31103106PLOT3D_FLD (by suitable OUTPUT command in the <span style="font-weight: bold;">mrun</span>
    3111 configuration file: &ldquo;<span style="font-family: monospace;">cat
    3112 PLOT3D_FLD_COOR &gt;&gt; PLOT3D_FLD</span>&rdquo;)
     3107configuration file: &#8220;<span style="font-family: monospace;">cat
     3108PLOT3D_FLD_COOR &gt;&gt; PLOT3D_FLD</span>&#8221;)
    31133109after PALM has
    31143110finished.&nbsp;To reduce the amount of data, output to this file
    … …  
    31473143respective files with suffix _GLOBAL (by
    31483144suitable OUTPUT commands in the <span style="font-weight: bold;">mrun</span>
    3149 configuration file, e.g.: &ldquo;<span style="font-family: monospace;">cat
    3150 PLOT2D_XY_LOCAL &gt;&gt; PLOT2D_XY_GLOBAL</span>&rdquo;)
     3145configuration file, e.g.: &#8220;<span style="font-family: monospace;">cat
     3146PLOT2D_XY_LOCAL &gt;&gt; PLOT2D_XY_GLOBAL</span>&#8221;)
    31513147after PALM has
    31523148finished. Cross sections can be directly plotted with <span style="font-weight: bold;">iso2d</span> using the
    … …  
    32283224default, all data (profiles, time
    32293225series, spectra, particle data, cross sections, volume data) are output
    3230 in NetCDF format (see chapter <a href="chapter_4.5.1.html">4.5.1</a>).
     3226in NetCDF 64bit-offset format (see chapter <a href="chapter_4.5.1.html">4.5.1</a>).
    32313227Exception: restart data (local files <a href="chapter_3.4.html#BININ">BININ</a>, <a href="chapter_3.4.html#BINOUT">BINOUT</a>, <a href="chapter_3.4.html#PARTICLE_RESTART_DATA_IN">PARTICLE_RESTART_DATA_IN</a>,
    32323228      <a href="chapter_3.4.html#PARTICLE_RESTART_DATA_OUT">PARTICLE_RESTART_DATA_OUT</a>)
    … …  
    32423238
    32433239The
    3244 numerical precision of the NetCDF output is determined with parameter <a href="#chapter_4.1.html#netcdf_precision">netcdf_precision</a>.<br>
    3245 
    3246 
    3247 
    3248 
    3249       <br>
    3250 
    3251 
    3252 
    3253 
    3254 The
    3255 maximum file size for NetCDF files is 2 GByte by default. Use the
    3256 parameter <a href="#netcdf_64bit">netcdf_64bit</a>
    3257 if larger files have to be created.<br>
     3240numerical precision of the NetCDF output is determined with parameter <a href="chapter_4.1.html#netcdf_precision">netcdf_precision</a>.<br>
     3241
     3242
     3243
     3244
     3245      <br>Other NetCDF formats (classic, NetCDF4/HDF5) can be selected with parameter <a href="#netcdf_data_format">netcdf_data_format</a>.<br>
    32583246
    32593247
    … …  
    84288416
    84298417 <tr>
    8430 
    8431 
    8432 
    8433 
    8434  <td style="vertical-align: top;"><a name="netcdf_64bit"></a><span style="font-weight: bold;">netcdf_64bit</span><br>
    8435 
    8436 
    8437 
    8438 
    8439 
     8418      <td style="vertical-align: top;"><span style="font-weight: bold;"><a name="netcdf_data_format"></a>netcdf_data_format</span><br>
    84408419      </td>
    8441 
    8442 
    8443 
    8444 
    8445  <td style="vertical-align: top;">L<br>
    8446 
    8447 
    8448 
    8449 
    8450  </td>
    8451 
    8452 
    8453 
    8454 
    8455 
    8456       <td style="vertical-align: top;"><span style="font-style: italic;">.F.</span><br>
    8457 
    8458 
    8459 
    8460 
    8461  </td>
    8462 
    8463 
    8464 
    8465 
    8466 
    8467       <td style="vertical-align: top;">All NetCDF files - except those containing 3d
    8468 volume data - will have 64
    8469 bit offset format if&nbsp;<span style="font-weight: bold;">netcdf_64bit</span>
    8470 = .TRUE..<br>
    8471 
    8472 
    8473 
    8474 
     8420      <td style="vertical-align: top;">I<br>
     8421      </td>
     8422      <td style="vertical-align: top;"><span style="font-style: italic;">2</span><br>
     8423      </td>
     8424      <td style="vertical-align: top;">Data format for NetCDF files.<br>
    84758425      <br>
    8476 
    8477 
    8478 
    8479 
    8480 By
    8481 default, the maximum file size of the NetCDF files opened by PALM is 2
    8482 GByte. Using <span style="font-weight: bold;">netcdf_64bit</span> = .TRUE. allows file sizes larger than 2
    8483 GByte.<br>
    8484 
    8485 
    8486 
    8487 
     8426This variable defines the format of the NetCDF files. Following values are allowed:<br>
    84888427      <br>
    8489 
    8490 
    8491 
    8492 
    8493 The 64 bit offset format for those NetCDF files containing 3d volume data (<span style="font-family: Courier New,Courier,monospace;">DATA_3D_NETCDF</span>,
    8494       <span style="font-family: Courier New,Courier,monospace;">DATA_3D_AV_NETCDF</span>)
    8495 is controlled independently by the switch <a href="#netcdf_64bit_3d">netcdf_64bit_3d</a>.<br>
    8496 
    8497 
    8498 
    8499 
     8428      <table style="text-align: left; width: 100%;" border="0" cellpadding="2" cellspacing="2">
     8429        <tbody>
     8430          <tr>
     8431            <td style="vertical-align: top;"><span style="font-style: italic;">1</span><br>
     8432            </td>
     8433            <td style="vertical-align: top;">NetCDF classic format (filesize limited to 2GB)<br>
     8434            </td>
     8435          </tr>
     8436          <tr>
     8437            <td style="vertical-align: top;"><span style="font-style: italic;">2</span><br>
     8438            </td>
     8439            <td style="vertical-align: top;">NetCDF 64-bit-offset format (large file support, but single variable still limited to 2GB)<br>
     8440            </td>
     8441          </tr>
     8442          <tr>
     8443            <td style="vertical-align: top;"><span style="font-style: italic;">3</span><br>
     8444            </td>
     8445            <td style="vertical-align: top;">NetCDF-4 (HDF5) format (files can be as large as file system supports; unlimited variable size; allows parallel I/O)<br>
     8446            </td>
     8447          </tr>
     8448          <tr>
     8449            <td style="vertical-align: top;"><span style="font-style: italic;">4</span><br>
     8450            </td>
     8451            <td style="vertical-align: top;">NetCDF-4 format, but with NF90_CLASSIC_MODEL bit set (some new features of NetCDF4 are not available)<br>
     8452            </td>
     8453          </tr>
     8454        </tbody>
     8455      </table>
    85008456      <br>
    8501 
    8502 
    8503 
    8504 
    8505       <span style="font-weight: bold;">Warning:</span><br>
    8506 
    8507 
    8508 
    8509 
    8510 Some
    8511 (PD or commercial) software may not support the 64 bit offset format.<br>
    8512 
    8513 
    8514 
    8515 
    8516 
     8457      <span style="font-weight: bold;">Important:</span><br>
     8458Setting <span style="font-weight: bold;">netcdf_data_format </span>&gt; <span style="font-style: italic;">2 </span>requires a NetCDF4 library (set <span style="font-family: Courier New,Courier,monospace;">-I</span>, <span style="font-family: Courier New,Courier,monospace;">-L</span>, and<span style="font-family: Courier New,Courier,monospace;"> -l </span>options for compiling and linking appropriately in configuration file). Also, preprocessor switch <span style="font-family: Courier New,Courier,monospace;">__netcdf4 </span>has to be set (see line starting with <span style="font-family: Courier New,Courier,monospace;">%cpp_opts </span>in the configuration file).<br>
     8459      <br>
     8460Files with NetCDF4 format cannot be read with NetCDF3 libraries.<br>
    85178461      </td>
    8518 
    8519 
    8520 
    8521 
    8522  </tr>
    8523 
    8524 
    8525 
    8526 
    8527     <tr>
    8528 
    8529 
    8530 
    8531 
    8532       <td style="vertical-align: top;"><a name="netcdf_64bit_3d"></a><span style="font-weight: bold;">netcdf_64bit_3d</span></td>
    8533 
    8534 
    8535 
    8536 
    8537       <td style="vertical-align: top;">L</td>
    8538 
    8539 
    8540 
    8541 
    8542       <td style="vertical-align: top;">.T.</td>
    8543 
    8544 
    8545 
    8546 
    8547       <td style="vertical-align: top;">NetCDF files containing 3d
    8548 volume data will have 64 bit offset format if&nbsp;<span style="font-weight: bold;">netcdf_64bit_3d</span>
    8549 = .TRUE..<br>
    8550 
    8551       <br>
    8552 
    8553 
    8554 
    8555 
    8556 By
    8557 default, the maximum file size of the NetCDF files opened by PALM is 2
    8558 GByte. Using <span style="font-weight: bold;">netcdf_64bit_3d</span> = .TRUE. allows file sizes larger than 2
    8559 GByte.<br>
    8560 
    8561       <br>
    8562 
    8563 
    8564 
    8565 
    8566 The 64 bit offset format for all other NetCDF files (<span style="font-style: italic;">not</span> containing 3d volume data) is controlled independently by the switch <a href="chapter_4.2.html#netcdf_64bit">netcdf_64bit</a>.<br>
    8567 
    8568       <br>
    8569 
    8570 
    8571 
    8572 
    8573       <span style="font-weight: bold;">Warning:</span><br>
    8574 
    8575 
    8576 
    8577 
    8578 Some
    8579 (PD or commercial) software may not support the 64 bit offset format.</td>
    8580 
    8581 
    8582 
    8583 
    85848462    </tr>
     8463
     8464
     8465
     8466
     8467
     8468   
    85858469
    85868470
    … …  
    87418625      <td style="vertical-align: top;">I</td>
    87428626
    8743       <td style="vertical-align: top;"></td>
     8627      <td style="vertical-align: top;"><br>
     8628</td>
    87448629
    87458630      <td style="vertical-align: top;">
    … …  
    88378722      <td style="vertical-align: top;">I</td>
    88388723
    8839       <td style="vertical-align: top;"></td>
     8724      <td style="vertical-align: top;"><br>
     8725</td>
    88408726
    88418727      <td style="vertical-align: top;">
    … …  
    1193811824user-interface (subroutine</span></font> <span style="font-family: monospace;">user_init_particles</span>)<span lang="en-GB"><font face="Thorndale, serif">.
    1193911825Particles can pull a
    11940 &ldquo;tail&rdquo; behind themselves to improve their
     11826&#8220;tail&#8221; behind themselves to improve their
    1194111827visualization.
    1194211828This is steered via the parameter&nbsp;<a href="chapter_4.2.html#use_particle_tails">use_particle_tails</a>.</font></span><a href="chapter_4.2.html#maximum_number_of_tailpoints"><span lang="en-GB"></span></a></p>
    … …  
    1199611882
    1199711883
    11998       <td style="vertical-align: top;"><i>&acute;reflect&acute;</i></td>
     11884      <td style="vertical-align: top;"><i>ŽreflectŽ</i></td>
    1199911885
    1200011886
    … …  
    1202111907default, particles are reflected at the bottom boundary.
    1202211908Alternatively, a particle absorption can set by <b>bc_par_b</b>
    12023 = <i>&acute;absorb&acute;</i>.</p>
     11909= <i>ŽabsorbŽ</i>.</p>
    1202411910
    1202511911
    … …  
    1206411950
    1206511951
    12066       <td style="vertical-align: top;"><i>&acute;cyclic&acute;</i></td>
     11952      <td style="vertical-align: top;"><i>ŽcyclicŽ</i></td>
    1206711953
    1206811954
    … …  
    1209011976are used along x.
    1209111977Alternatively, reflection (<b>bc_par_lr</b>
    12092 = <i>&acute;reflect&acute;</i>) or absorption (<b>bc_par_lr</b>
    12093 = <i>&acute;absorb&acute;</i>)
     11978= <i>ŽreflectŽ</i>) or absorption (<b>bc_par_lr</b>
     11979= <i>ŽabsorbŽ</i>)
    1209411980can be set. <br>
    1209511981
    … …  
    1215212038
    1215312039
    12154       <td style="vertical-align: top;"><i>&acute;cyclic&acute;</i></td>
     12040      <td style="vertical-align: top;"><i>ŽcyclicŽ</i></td>
    1215512041
    1215612042
    … …  
    1217812064are used along y.
    1217912065Alternatively, reflection (<b>bc_par_ns</b>
    12180 = <i>&acute;reflect&acute;</i>) or absorption (<b>bc_par_ns</b>
    12181 = <i>&acute;absorb&acute;</i>)
     12066= <i>ŽreflectŽ</i>) or absorption (<b>bc_par_ns</b>
     12067= <i>ŽabsorbŽ</i>)
    1218212068can be set.<br>
    1218312069
    … …  
    1223012116
    1223112117
    12232       <td style="vertical-align: top;"><i>&acute;absorb&acute;</i></td>
     12118      <td style="vertical-align: top;"><i>ŽabsorbŽ</i></td>
    1223312119
    1223412120
    … …  
    1225512141particles are absorbed at the top boundary.
    1225612142Alternatively, a reflection condition can be set by <b>bc_par_t</b>
    12257 = <i>&acute;reflect&acute;</i>.</p>
     12143= <i>ŽreflectŽ</i>.</p>
    1225812144
    1225912145
    … …  
    1432414210
    1432514211 <td style="vertical-align: top;">Rear
    14326 (&ldquo;north&rdquo;) edge of a
     14212(&#8220;north&#8221;) edge of a
    1432714213particle source (in m). </td>
    1432814214
    … …  
    1442414310
    1442514311 <td style="vertical-align: top;">Front
    14426 (&ldquo;south&rdquo;) edge of a
     14312(&#8220;south&#8221;) edge of a
    1442714313particle source (in m). </td>
    1442814314
    … …  
    1461414500     
    1461514501     
    14616       <p><span style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"><font color="#000000">Initial position of the</font></span>
     14502      <p><span style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;"><font color="#000000">Initial position of the</font></span>
    1461714503particles is
    1461814504varied randomly within certain limits.&nbsp; </p>
    … …  
    1629016176(cross sections), and <span style="font-style: italic;">'particles'</span>.
    1629116177Within the strings the hash characters ("##") have to be replaced by two
    16292 digits 01&le;##&le;99. Up to 10 objects
     16178digits 01&#8804;##&#8804;99. Up to 10 objects
    1629316179can be assigned at the same time, e.g.:&nbsp; </p>
    1629416180
    … …  
    1735317239subsequent columns. </font>The order
    1735417240of the data in the file follows the order used in the assignment for <b>data_output_sp</b>
    17355 (<b>data_output_sp</b> = <span style="font-style: italic;">'u'</span>, <span style="font-style: italic;">'v'</span>,&hellip;
     17241(<b>data_output_sp</b> = <span style="font-style: italic;">'u'</span>, <span style="font-style: italic;">'v'</span>,&#8230;
    1735617242means that the file starts with the spectra of the u-component,
    1735717243followed by the v-component spectra, etc.). Additional to the files
    … …  
    1774817634
    1774917635
    17750 </body>
    17751 </html>
     17636
     17637</body></html>
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