Tool Box Venus PCM - Revision history

Rcapron: /* LMDZ.VENUS/Tools */

2024-08-14T10:00:02Z

‎LMDZ.VENUS/Tools

Rcapron: /* Main programs (other than GCM) but included in the Venus PCM package */

2024-08-14T09:23:23Z

‎Main programs (other than GCM) but included in the Venus PCM package

Emillour at 17:13, 4 August 2024

2024-08-04T17:13:43Z

Emillour at 16:45, 4 August 2024

2024-08-04T16:45:16Z

Emillour at 23:41, 2 August 2024

2024-08-02T23:41:13Z

Emillour: Created page with "== Post-processing tools provided with the Venus PCM == First and foremost there are a number of postprocessing utilities (self-standing tools) which can be found in the ''UTI..."

2024-08-02T23:39:40Z

Created page with "== Post-processing tools provided with the Venus PCM == First and foremost there are a number of postprocessing utilities (self-standing tools) which can be found in the ''UTI..."

New page

== Post-processing tools provided with the Venus PCM ==
First and foremost there are a number of postprocessing utilities (self-standing tools) which can be found in the ''UTIL'' and ''LMDZ.VENUS/Tools'' directories. Secondly one has some extra main programs in the dynamics-physics interface.

=== UTIL ===

=== LMDZ.VENUS/Tools ===

=== Main programs (other than GCM) but included in the Venus PCM package ===
There are a few other main programs that are included with the GCM.

Advanced stuff: these main programs are located under ''LMDZ.VENUS/dynphy_lonlat/phyvenus/'' as they are at the interface between lon-lat dynamics and the Venus physics package

==== start2archive ====

==== newstart ====

== The rcm1d 1D column program ==
The source code is located under ''LMDZ.VENUS/libf/phyvenus/dyn1d''

... Compilation...

[[Category:Venus-Model]]

← Older revision		Revision as of 10:00, 14 August 2024
Line 19:		Line 19:

	The ''startarchive2icosa'' subdirectory contains some programs and instructions (see the README there) to generate a DYNAMICO-Venus set of start files from a lon-lat <code>start_archive.nc</code> file		The ''startarchive2icosa'' subdirectory contains some programs and instructions (see the README there) to generate a DYNAMICO-Venus set of start files from a lon-lat <code>start_archive.nc</code> file
		+
		+	==== Using angmom ====
		+	First, one need to compile the subprograms using this script :
		+	<pre>
		+	#!/bin/bash
		+
		+	# Source
		+	source /chemin/vers/votre/XIOS/arch.env
		+	source /chemin/vers/votre/XIOS/arch.path
		+
		+	# Chemins NetCDF
		+	NETCDF_INCLUDE=$NETCDF_INCDIR
		+	NETCDF_LIB=$NETCDF_LIBDIR
		+
		+	# Compilation des sous-programmes
		+	mpif90 -c -g -traceback cpdet.F90 moyzon.F moyzon2.F moytim.F dx_dp.F epflux.F90 io.F90 dmass.F90 reverse.F90 \
		+	$NETCDF_INCLUDE $NETCDF_LIB
		+	</pre>
		+
		+	Then, compile the main programs with this script :
		+	<pre>
		+	#!/bin/bash
		+
		+	# Source
		+	source /chemin/vers/votre/XIOS/arch.env
		+	source /chemin/vers/votre/XIOS/arch.path
		+
		+	# Chemins NetCDF
		+	NETCDF_INCLUDE=$NETCDF_INCDIR
		+	NETCDF_LIB=$NETCDF_LIBDIR
		+
		+
		+	main_programs=("stability.F90" "energy.F90" "psi.F90" "tem.F90" "angmom.F90" "tmc.F90")
		+
		+	for program in "${main_programs[@]}"; do
		+	program_name=$(basename "$program" .F90)
		+	mpif90 -g -traceback "$program" *.o \
		+	-I /chemin/vers/votre/XIOS/inc -L /chemin/vers/votre/XIOS/lib -lxios -lstdc++ \
		+	$NETCDF_INCLUDE $NETCDF_LIB -o "${program_name}.e"
		+	done
		+
		+	\rm *.o
		+	</pre>
		+
		+	Be aware that, if you modify a one of the main programs and wish to re-compile it, don't forget to re-compile the subprograms first. Without, you'll end up with an issue, that the script cannot find the .o files needed for the compilation.
		+
		+	After doing this, you should obtain the executable <code>angmom.e</code>. Copy it in the repository that contains the NetCDF files that you want to analyse.
		+	<pre>
		+	cp ../../your/path/
		+	</pre>
		+
		+	Then execute it
		+	<pre>
		+	./angmom.e
		+	</pre>
		+
		+	When the program is run, you will first be asked for the name of the file you wish to use. Write it down and then type enter.
		+	You will then be asked if you wish to use the file "dynzon.nc". If you don't want to, simply type "enter".
		+
		+	Normally, at the end of execution, you should obtain a file called "your_file_GAM.nc" (if the original name was "your_file.nc").
		+
		+	'''Nota Bene :'''
		+	Here is a modified "alternative" script of angmom.F90, that don't take into account the <code>dyzon.nc</code> file, and, which is run only by this command :
		+	<pre>
		+	./angmom.e your_file.nc
		+	</pre>
		+
		+	This is a way more practical use of it.
		+
		+	'''Nota Bene 2 :'''
		+	If you use angmom on a file that is a bit heavy, you will probably get an execution error, specifying that the machine has not been able to allocate enough memory. To remedy this, simply run a job in a compute node. The advantage of '''Nota Bene 1''' is that it is easier to run the program in a compute node that is not necessarily interactive (using the "alternative" script).
		+
		+	Example of script job submission in this case (simply use <code>sbatch your_submission_script</code>) :
		+	<pre>
		+	#!/bin/bash
		+	#SBATCH --nodes=1
		+	#SBATCH --ntasks-per-node=1
		+	#SBATCH --partition=zen16
		+	#SBATCH --mem=24G
		+	#SBATCH -J job_angmom
		+	#SBATCH --time=1:00:00
		+	#SBATCH --output=job_angmom.%j.out
		+
		+
		+	source /your/path/trunk/ARCH/arch-ifort_MESOIPSL.env
		+
		+
		+	./angmom.e your_file.nc > angmom.out 2>&1
		+	</pre>
		+	You can follow the run of the program in angmom.out, using for example <code>tail -f angmom.out</code>.

	== Main programs (other than GCM) but included in the Venus PCM package ==		== Main programs (other than GCM) but included in the Venus PCM package ==

@@ Line 23: / Line 23: @@
 There are a few other main programs that are included with the GCM.
-Advanced stuff: these main programs are located under ''LMDZ.VENUS/dynphy_lonlat/phyvenus/'' as they are at the interface between lon-lat dynamics and the Venus physics package
+Advanced stuff: these main programs are located under ''LMDZ.VENUS/libf/dynphy_lonlat/phyvenus/'' as they are at the interface between lon-lat dynamics and the Venus physics package
 === start2archive ===
@@ Line 36: / Line 36: @@
 * Compiling <code>newstart</code> is done using the [[The makelmdz fcm GCM Compilation Script|makelmdz_fcm]] utility. The program is then meant to be run interactively with the user providing options and choices when prompted.
 * Once the program has run and finished without error, it will generate <code>restart.nc</code> and <code>restartfi.nc</code>
 == The rcm1d 1D column program ==

@@ Line 3: / Line 3: @@
 === UTIL ===
 === LMDZ.VENUS/Tools ===
 == Main programs (other than GCM) but included in the Venus PCM package ==