Tool Box - Revision history

Emillour at 13:38, 4 February 2026

2026-02-04T13:38:59Z

Jbclement at 13:01, 7 July 2025

2025-07-07T13:01:58Z

Jbclement at 13:00, 7 July 2025

2025-07-07T13:00:04Z

Jbclement: Update about version argument for programs

2025-07-07T12:57:54Z

Update about version argument for programs

Jbclement: /* Identifying the code version of an executable file */

2025-01-23T08:38:44Z

‎Identifying the code version of an executable file

Jbclement: /* Identifying the code version of an executable */

2025-01-23T08:37:41Z

‎Identifying the code version of an executable

Jbclement: Explanations of the feature allowing to know the compilation and version details of the executable

2025-01-23T08:25:08Z

Explanations of the feature allowing to know the compilation and version details of the executable

LTeinturier: /* XARRAY python library (more modern) */

2023-12-07T10:52:26Z

‎XARRAY python library (more modern)

LTeinturier: /* XARRAY python library (more modern) */

2023-12-07T10:51:28Z

‎XARRAY python library (more modern)

Martin.turbet: /* newstart: a fortran program to modify start files */

2023-11-07T15:51:36Z

‎newstart: a fortran program to modify start files

@@ Line 6: / Line 6: @@
 To be usable, ''newstart'' should be compile in the ''LMDZ.COMMON'' directory by using the following command line:
 <syntaxhighlight lang="bash">
-./makelmdz_fcm -arch my_arch_file -p std -d 64x48x30 newstart
+./makelmdz_fcm -arch my_arch_file -p generic -d 64x48x30 newstart
 </syntaxhighlight>
 In the example, my_arch_file is the name the arch files (see [https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/The_Target_Architecture_(%22arch%22)_Files arch] ) and 64x48x30 is the resolution of the physical grid.
@@ Line 20: / Line 20: @@
 The command line to compile start2archive is similar to the one used for newstart:
 <syntaxhighlight lang="bash">
-./makelmdz_fcm -arch my_arch_file -p std -d 64x48x30 start2archive
+./makelmdz_fcm -arch my_arch_file -p generic -d 64x48x30 start2archive
 </syntaxhighlight>
 To modify the resolution, you should first create a start_archive (by using start2archive) file at the used resolution, then compile a newstart file at the new resolution. Newstart will interpolate all the physical quantities on the new grid.
@@ Line 168: / Line 168: @@
 # Run GCM -- THIS LINE NEEDS TO BE MODIFIED WITH THE CORRECT GCM EXECUTION COMMAND
-mpirun -np 8 gcm_64x48x26_phystd_para.e < diagfi.def > lrun${numnew}
+mpirun -np 8 gcm_64x48x26_phygeneric_para.e < diagfi.def > lrun${numnew}

@@ Line 256: / Line 256: @@
 call parse_args()
 </syntaxhighlight>
-Don't forget to add the module as well:
+Don't forget to add the required module as well:
 <syntaxhighlight lang="bash">
 use parse_args_mod, only: parse_args

@@ Line 242: / Line 242: @@
 </syntaxhighlight>
-== Identifying the code version of an executable file ==
+== Printing the code version of a program ==
 Details about compilation and code version (SVN or Git) are embedded in the executable file. This feature helps track code builds and their exact compilation context directly from the executable.

@@ Line 244: / Line 244: @@
 == Identifying the code version of an executable file ==
-Details about compilation and code version (SVN or Git) are embedded in the executable file. To display these information, put the argument 'version' as an option when executing the code such as:
+Details about compilation and code version (SVN or Git) are embedded in the executable file. This feature helps track code builds and their exact compilation context directly from the executable.
 <syntaxhighlight lang="bash">
-./executable.e version
+./myprogram.e --version [file]
 </syntaxhighlight>
-It shows in the terminal the date and the command of compilation as well as the version control information for the sub-folders of your trunk if applicable. In addition, it creates a file called "version_stat-diff.txt" containing the result of status and diff commands between the code repository and your local copy which produced the executable file.
+This will write compilation and version details into the specified [file]. If [file] is omitted, the default name "pgrm_version_details.txt" will be used. The file contains compilation details, the version control information (SVN or Git), the status and the diff result if applicable, for the sub-folders of your trunk.
 This feature is available for every program of the Mars model, the Generic model and the PEM. If you want to extend it to other models, please add the following code section at the beginning of your main programs:
 <syntaxhighlight lang="bash">
-if (command_argument_count() > 0) then ! Get the number of command-line arguments
+! Parse command-line options
-    call get_command_argument(1,arg) ! Read the argument given to the program
+call parse_args()
 </syntaxhighlight>
-As well as the necessary declaration and module:
+Don't forget to add the module as well:
 <syntaxhighlight lang="bash">
-use version_info_mod, only: print_version_info
+use parse_args_mod, only: parse_args
 </syntaxhighlight>

@@ Line 248: / Line 248: @@
 ./executable.e version
 </syntaxhighlight>
-It shows in the terminal the date and the command of compilation as well as the version control information for the sub-folders of your trunk if applicable. In addition, it creates a file called "version_stat-diff.txt" containing the result of status and diff commands between the code repository and the local copy which produced the executable file.
+It shows in the terminal the date and the command of compilation as well as the version control information for the sub-folders of your trunk if applicable. In addition, it creates a file called "version_stat-diff.txt" containing the result of status and diff commands between the code repository and your local copy which produced the executable file.
 This feature is available for every program of the Mars model, the Generic model and the PEM. If you want to extend it to other models, please add the following code section at the beginning of your main programs:
 <syntaxhighlight lang="bash">

← Older revision		Revision as of 08:25, 23 January 2025
Line 242:		Line 242:
	</syntaxhighlight>		</syntaxhighlight>

		+	== Identifying the code version of an executable ==
		+
		+	It is possible to track compilation and version (SVN or Git) details of the code which produced the executable file. For this, put the argument 'version' as an option when executing the code:
		+	<syntaxhighlight lang="bash">
		+	./executable.e version
		+	</syntaxhighlight>
		+	It shows in the terminal the date and the command of compilation as well as the version control information for the sub-folders of your trunk if applicable. In addition, it creates a file "version_stat-diff.txt" containing the status and diff results between the local copy and the repository of the code which produced the executable file.
		+	This feature is available for every program of the Mars model, the Generic model and the PEM. If you want to extend it to other models, please add the following code section at the beginning of your main programs:
		+	<syntaxhighlight lang="bash">
		+	if (command_argument_count() > 0) then ! Get the number of command-line arguments
		+	call get_command_argument(1,arg) ! Read the argument given to the program
		+	select case (trim(adjustl(arg)))
		+	case('version')
		+	call print_version_info()
		+	stop
		+	case default
		+	error stop "The argument given to the program is unknown!"
		+	end select
		+	endif
		+	</syntaxhighlight>
		+	As well as the necessary declaration and module:
		+	<syntaxhighlight lang="bash">
		+	use version_info_mod, only: print_version_info
		+	</syntaxhighlight>
		+	<syntaxhighlight lang="bash">
		+	character(100) :: arg ! To read command-line arguments
		+	</syntaxhighlight>

	== Processing Output Files with NCOs ==		== Processing Output Files with NCOs ==

@@ Line 469: / Line 469: @@
 data = xr.open_dataset(file,decode_times=False)
 print(data)
-##extracting the altitude level # for the whole file
+##extracting the altitude level #20 for the whole file
 data = data.isel(altitude=20)
 ##let's assume that data hold a time-series of the temperature. Let's average it in time
-temp = data['temp'].mean("Time",keep_attrs=True) #we keep the attribute when averaging
+temp = data['temp'].mean("Time",keep_attrs=True) #we keep the attribute when averaging to conserve the DataArray structure
 ##now we plot
 fig = temp.plot.contourf(cmap='gnuplot',levels=50) #choose the colormap and the number of contourf levels

← Older revision		Revision as of 10:51, 7 December 2023
Line 459:		Line 459:

	</syntaxhighlight>		</syntaxhighlight>
		+
		+	One cool thing about xarray is that it is well optimized, and can do whatever you want to do on your data, but better than you. See for instance, the example below to plot a temperature lon-lat map. Xarray handles it in 5 lines of code, where you would need a lot more to set-up you plot in traditional matplotlib. And the results look almost good enough for a paper plot.
		+
		+	<syntaxhighlight lang="python" line>
		+	import xarray as xr
		+	import matplotlib.pyplot as plt
		+	##Load your data and print it
		+	file = '/home/lteinturier/Documents/PhD/wasp43b/chemistry_project/input_5xsolar.nc'
		+	data = xr.open_dataset(file,decode_times=False)
		+	print(data)
		+	##extracting the altitude level # for the whole file
		+	data = data.isel(altitude=20)
		+	##let's assume that data hold a time-series of the temperature. Let's average it in time
		+	temp = data['temp'].mean("Time",keep_attrs=True) #we keep the attribute when averaging
		+	##now we plot
		+	fig = temp.plot.contourf(cmap='gnuplot',levels=50) #choose the colormap and the number of contourf levels
		+	fig.ax.set_title("P = {:.2e} mbar".format(data.p.mean().values)) ##set-up your title. If you don't change it, the title will be the altitude in km of your atmospheric level
		+	plt.show()
		+
		+	</syntaxhighlight>
		+	This is only a fraction of what Xarray can do. Check the [https://docs.xarray.dev/en/stable/user-guide/index.html documentation] for more.

	==== Python tutorials to make pretty visuals ====		==== Python tutorials to make pretty visuals ====

@@ Line 13: / Line 13: @@
 When you execute newstart, you can use both a ''start2archive'' file or the start files (''start.nc'' and ''startfi.nc''). Then the interactive interface will propose to modify several physical quantities such as the gravity, the surface pressure or the rotation of the planet. At the end of the procedure, two files are created: '' '''re'''start.nc'' and '' '''re'''startfi.nc''. They can be renamed and used as start files to initialize a new simulation.
-We have prepared a simple tutorial to learn how to modify ''start.nc'' and ''startfi.nc'' files (= the the initial conditions) for the Generic PCM: https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/Modify_start_Files#Using_newstart.e_routine
+We have prepared a simple tutorial to learn how to modify ''start.nc'' and ''startfi.nc'' files (= the the initial conditions) for the Generic PCM: https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/Modify_start_Files
 === start2archive ===