== PALM Source Code !ChangeLog ==

Current revision:  [[CRev]]

||='''Date'''  =||='''Author'''  =||='''svn\\Revision'''  =||='''Last\\Release'''  =||='''Type''' =||='''Description''' =||
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09/09/10
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{{{#!td style="vertical-align:top;width: 50px"
CH
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{{{#!td style="vertical-align:top;width: 75px"
r560
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
B
}}}
{{{#!td style="vertical-align:top"
Bugfix of calculating ngp_3d for 64 bit. So far ngp_3d  has not been 64 bit.
}}}
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{{{#!td style="vertical-align:top;width: 50px"
07/09/10
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{{{#!td style="vertical-align:top;width: 50px"
CH
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{{{#!td style="vertical-align:top;width: 75px"
r557
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
B
}}}
{{{#!td style="vertical-align:top"
Bugfix for message string in if statement (dz_stretch_level) of subroutine {{{set_mask_locations}}}.

The change concerns the masked data output, which is still not documented.
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07/09/10
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SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r556
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{{{#!td style="vertical-align:top"
3.7a
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{{{#!td style="vertical-align:top"
C
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Documentation for surface_heatflux in case of {{{prandtl_layer}}} = ''.F.'' improved.

bugfix for wrong netcdf/3.6.3 module on lcsgi (mbuild, mrun)
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}}}
{{{#!td style="vertical-align:top"
B
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{{{#!td style="vertical-align:top"
Bugfix in if statement (disturb_heatflux)

Bugfix: in 2201 statement: closing " was missing (interpret_config)

Bugfix: default setting of nzb_local for flat topography (init_grid)

Bugfix: wrong dimension used for ts_value_l (user_statistics)
}}}
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01/09/10
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{{{#!td style="vertical-align:top;width: 50px"
CH
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{{{#!td style="vertical-align:top;width: 75px"
r553
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3.7a
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{{{#!td style="vertical-align:top"
C
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d3dpar-parameters for masked output {{{data_output_mask_*}}}, {{{data_output_mask_user_*}}}, {{{mask_*_x}}}, {{{mask_*_y}}}, {{{mask_*_z}}}, {{{mask_*_x_loop}}}, {{{mask_*_y_loop}}} and {{{mask_*_z_loop}}} have been replaced by corresponding (array-) parameters {{{data_output_masks}}}, {{{data_output_masks_user}}}, {{{mask_x}}}, {{{mask_y}}}, {{{mask_z}}}, {{{mask_x_loop}}}, {{{mask_y_loop}}}, and {{{mask_z_loop}}}.

inipar-parameter {{{masks}}} has been removed.

The changes concern the masked data output, which is still not documented.
}}}
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17/08/10
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BM
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r544
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{{{#!td style="vertical-align:top"
3.7a
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N/C/B
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new: {{{.mrun.config.lcxt4}}} for Cray-XT4 in !Bergen/Norway

changes: adjustments for lcxt4

bugfix: loading of user-defined modules (mbuild)
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15/06/10
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RH
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{{{#!td style="vertical-align:top;width: 75px"
r540
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{{{#!td style="vertical-align:top"
3.7a
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{{{#!td style="vertical-align:top"
C
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ssh from compute nodes to login nodes on hosts lcsgih/lcsgib is done using the names hicegate0/bicegate0 instead of the IP addresses
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21/04/10
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{{{#!td style="vertical-align:top;width: 50px"
RH
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{{{#!td style="vertical-align:top;width: 75px"
r532
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{{{#!td style="vertical-align:top"
3.7a
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{{{#!td style="vertical-align:top"
C
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Large scale vertical motion (subsidence/ascent) can be added as additional source to the prognostic equation for humidity/passive scalar.
 
Character length for dopr_unit enlarged.

Adjustment of the NCL scripts to allow for output of png files. 
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}}}
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}}}
{{{#!td style="vertical-align:top"
B
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Bugfix: unit of hyp changed to dbar (check_parameters)
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{{{#!td style="vertical-align:top;width: 50px"
01/04/10
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{{{#!td style="vertical-align:top;width: 50px"
RH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r530
}}}
{{{#!td style="vertical-align:top"
3.7a
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{{{#!td style="vertical-align:top"
B
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Bugfix: treatment of special character * in NCL variables containing lists corrected
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31/03/10
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{{{#!td style="vertical-align:top;width: 50px"
RH
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{{{#!td style="vertical-align:top;width: 75px"
r529
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{{{#!td style="vertical-align:top"
3.7a
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{{{#!td style="vertical-align:top"
C
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List of variable names have to be specified using blank separated lists and single quotes
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{{{#!td style="vertical-align:top;width: 50px"
30/03/10
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{{{#!td style="vertical-align:top;width: 50px"
RH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r526
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
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Adjustment of the NCL scripts and {{{palmplot}}} to allow for special characters in netCDF variable names.
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30/03/10
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{{{#!td style="vertical-align:top;width: 50px"
SR
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{{{#!td style="vertical-align:top;width: 75px"
r525
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
B
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Bugfix: "/" in netcdf profile variable names replaced by ":"
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19/03/10
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{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r520
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
N
}}}
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netCDF4 support for particle data. Total number of particles is allowed to increase during the run, when {{{netcdf_data_format}}} > 2  is used.
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{{{#!td style="vertical-align:top;width: 75px"

}}}
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}}}
{{{#!td style="vertical-align:top"
C
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Special characters like * and " are now allowed for netCDF variable names. Replacement of these characters has been removed (routine {{{clean_netcdf_varname}}} removed)
}}}
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18/03/10
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{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r516
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
N
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Simple installation method has been documented (see [wiki:doc/install]). Respective scripts and configuration files have been updated.
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}}}
{{{#!td style="vertical-align:top"
B
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opt=1 is forced for PGI-compiler in routine {{{buoyancy}}} by compiler-directive. Otherwise, program aborts with SIGFPE.
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16/03/10
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{{{#!td style="vertical-align:top;width: 50px"
RH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r513
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
N
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NCL scripts can be run with the shell script {{{palmplot}}}.
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12/03/10
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SR
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{{{#!td style="vertical-align:top;width: 75px"
r509
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
B
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bugfix for r504: remode_md was given a wrong value
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08/03/10
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{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r506
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
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hack for better usage of '''mrun''' on Kyoto computing center machine (lckyoto)
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03/03/10
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{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r504
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
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{{{combine_plot_fields}}} is now directly called within '''mrun''' and must not be given by an output command in the configuration file any more. Please remove the respective output command ({{{OC:combine_plot_fields.x}}}) from your configuration file!

Utility programs ({{{combine_plot_fields}}}, {{{interpret_config}}}) are created by '''mbuild''' separately for each block in the configuration file. Depending on option {{{-K}}}, '''mrun''' is using the utility programs for the respective block.

Utility programs are also compiled in parallel, depending on variable {{{%mopts}}} in the configuration file..

Default configuration files updated.
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02/03/10
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{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r496
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
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Particle data for restart runs are only written if environment variable {{{write_binary}}} = ''.T.'', i.e. particle data are now handled in the same way as the other restart data. (palm)
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01/03/10
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{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r494
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
N
}}}
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Output in netCDF4-format.

netCDF4 allows for parallel I/O. Also, variables are not limited in size any more (i.e. arrays can be larger than 2GB). The new d3par-parameter [wiki:/doc/app/d3par#netcdf_data_format netcdf_data_format] can be used to select among the different netCDF file formats (1: classic format, 2: 64-bit-offset format (this is now the default), 3: netCDF4/HDF5 format, 4: netCDF4 format with NF90_CLASSIC_MODEL bit set). Setting {{{netcdf_data_format}}} > 2 only affects 2d- and 3d-output, i.e. there is no parallel output for profiles, time series, spectra, and particles. Parallel output of particle data may be realized in the future.

In case of parallel output, all PEs write into one file, which means that postprocessing the data with {{{combine_plot_fields}}} (merging data from single files - one per PE - into one file) is not neccessary. In this case, flag files are automatically set, telling {{{combine_plot_fields}}} that nothing is to be done.

Using netCDF4 format requires a netCDF4/HDF5 library. Respective settings for {{{-I}}}, {{{-L}}}, and {{{-l}}} compiler/loader options for the SGI-ICE at HLRN can be found in the new example configuration file [source:palm/trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4 .mrun.config.imuk_ice2_netcdf4]

'''Attention:'''
So far, netCDF parallel I/O has only been tested a little. Further performance optimizations may be required, especially in case of large data sets (e.g. data chunking, or lustre file system settings with {{{lfs setstripe}}}). Please report bugs and performance problems immediately!

{{{combine_plot_fields}}} outputs cpu-time needed for file merging.

Modules to be loaded for compilation ('''mbuild''') or job execution ('''mrun''') can/should now be given in the configuration file ({{{.mrun.config}}}) 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 and remove the {{{%mpilib}}} variable in your configuration file.

Compilation time can be reduced be using parallel make. The number of allowed simultaneous compiler calls (threads) is set in the configuration file using variable {{{%mopt}}}, e.g.
{{{
   %mopts  -j:4   lcsgih parallel
}}}
allows a maximum of 4 routines to be compiled simultaneously (provided that the makefile does not show any dependencies between these routines).
}}}
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{{{#!td style="vertical-align:top"
C
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d3par-parameters {{{netcdf_64bit}}} and {{{netcdf_64bit_3d}}}  have been removed. Use the new d3par-variable {{{netcdf_data_format}}} = 2 for choosing the netCDF 64bit-offset format (this is the default from now on). The offset-format can not be set independently for the 3d-output-data any more.

d3par-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}}}. This change concerns the masked data output, which is still not documented.
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}}}
{{{#!td style="vertical-align:top"

}}}
{{{#!td style="vertical-align:top"
B
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{{{#!td style="vertical-align:top"
Bugfix in [source:palm/trunk/UTIL/Makefile Makefile]: forgot to compile for {{{interpret_config}}}.

Bugfix: timeseries data have to be collected by PE0 (user_statistics).
}}}
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05/02/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r484
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
B
}}}
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{{{ngp_3d}}}, {{{ngp_3d_inner}}}  changed to 64 bit. Otherwise, on large grids > 2*10^9^ grid points some global statistics (e.g. total kinetic energy) have wrong values.
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