LMDZPedia - Contributions de l’utilisateur [fr]

RunningDYNAMICO

2022-05-13T13:52:11Z

Dubos : /* Running DYNAMICO */

= Running DYNAMICO =

DYNAMICO can produce a rather large amount of output. It is therefore recommended to prepare a separate directory for each numerical experiment on a filesystem of adequate capacity.
In this directory, copy the executable icosa_gcm.exe. You will find it in DYNAMICO/bin/, where DYNAMICO is the main directory containing the source code.

You will also need configuration files that define resolution, initial condition, etc. Sample files can be found in subdirectories of [source:codes/icosagcm/trunk/param_sets DYNAMICO/param_sets]. Copy the *.def files from the desired sub-directory. There is typically run.def and earth_const.def . run.def is the main configuration file and includes earth_const.def

Currently DYNAMICO generates its own grid. It can run idealized test cases which define their own initial conditions. In that case no other input files are needed beyond *.def and, if using XIOS, *.xml files controlling XIOS behavior. It may also restart from a previous run, reading from a restart file.

== IMPORTANT ==
Make sure you set
<pre>
ulimit -s unlimited
</pre>
before running DYNAMICO in order to avoid stack overflows (segmentation faults) due to large automatic arrays. With OpenMP:
<pre>
export OMP_STACK_SIZE=100M
</pre>
or a larger value if necessary.

== Running DYNAMICO as a primitive equation solver ==

By default DYNAMICO solves the traditional, shallow-atmosphere, hydrostatic equations. An example is provided in [https://gitlab.in2p3.fr/ipsl/projets/dynamico/dynamico/-/blob/trunk2master/param_sets/dcmip2012/run41.def param_sets/dcmip2012/run41.def]. This example runs a dry baroclinic instability test case (Jablonowski & Williamson, 2006). Sample configuration files for the climate-like Held and Suarez (1994) benchmark can be found in [https://gitlab.in2p3.fr/ipsl/projets/dynamico/dynamico/-/tree/trunk2master/param_sets/climate/Held_Suarez param_sets/climate/Held_Suarez]

== Horizontal resolution ==

Horizontal resolution is controlled by the parameter nbp defined in run.def. The total number of hexagonal cells is about 10 x nbp x nbp, corresponding to subdividing each main triangle of the icosahedron in nbp x nbp sub-triangles (there are about twice as many triangles as there are hexagons).
Notice that, everything else being equal, the time step (dt) should be inversely proportional to nbp for numerical stability.

== Parallel computing with DYNAMICO ==

DYNAMICO can run in parallel by dividing the icosahedral mesh into tiles. There are at least 10 tiles corresponding to the 20 faces of the icosahedron joined in pairs to form rhombi. These 10 rhombi are further subdivided in nsplit_i x nsplit_j tiles. nsplit_i and nsplit_j are defined in run.def . nsplit_X needs not divide nbp exactly.

To run DYNAMICO on a parallel machine, you must first compile it with OpenMPI and/or MPI. Then use mpirun or the equivalent command to run it.
There must be less MPIxOpenMP processes than the 10 x nsplit_i x nsplit_j tiles. There can be more tiles than processes, in which case each process will take care of several tiles.

[[Category:DYNAMICO]]

RunningDYNAMICO

2022-05-13T13:47:22Z

Dubos : Page créée avec « = Running DYNAMICO = DYNAMICO can produce a rather large amount of output. It is therefore recommended to prepare a separate directory for each numerical experiment on a... »

= Running DYNAMICO =

DYNAMICO can produce a rather large amount of output. It is therefore recommended to prepare a separate directory for each numerical experiment on a filesystem of adequate capacity.
In this directory, copy the executable icosa_gcm.exe. You will find it in DYNAMICO/bin/, where DYNAMICO is the main directory containing the source code.

You will also need configuration files that define resolution, initial condition, etc. Sample files can be found in subdirectories of [source:codes/icosagcm/trunk/param_sets DYNAMICO/param_sets]. Copy the *.def files from the desired sub-directory. There is typically run.def and earth_const.def . run.def is the main configuration file and includes earth_const.def

Currently DYNAMICO generates its own grid. It can run idealized test cases which define their own initial conditions. In that case no other input files are needed beyond *.def and, if using XIOS, *.xml files controlling XIOS behavior. It may also restart from a previous run, reading from a restart file.

== IMPORTANT ==
Make sure you set
<pre>
ulimit -s unlimited
</pre>
before running DYNAMICO in order to avoid stack overflows (segmentation faults) due to large automatic arrays. With OpenMP:
<pre>
export OMP_STACK_SIZE=100M
</pre>
or a larger value if necessary.

== Running DYNAMICO as a primitive equation solver ==

By default DYNAMICO solves the traditional, shallow-atmosphere, hydrostatic equations. An example is provided in [source:codes/icosagcm/trunk/param_sets/dcmip2012/ dcmip2012/test4/test4.1/test4.1-0 ]. This example runs a dry baroclinic instability test case (Jablonowski & Williamson, 2006). Sample configuration files for the climate-like Held and Suarez (1994) benchmark can be found in [source:codes/icosagcm/trunk/param_sets/climate/Held_Suarez climate/Held_Suarez ]

== Horizontal resolution ==

Horizontal resolution is controlled by the parameter nbp defined in run.def. The total number of hexagonal cells is about 10 x nbp x nbp, corresponding to subdividing each main triangle of the icosahedron in nbp x nbp sub-triangles (there are about twice as many triangles as there are hexagons).
Notice that, everything else being equal, the time step (dt) should be inversely proportional to nbp for numerical stability.

== Parallel computing with DYNAMICO ==

DYNAMICO can run in parallel by dividing the icosahedral mesh into tiles. There are at least 10 tiles corresponding to the 20 faces of the icosahedron joined in pairs to form rhombi. These 10 rhombi are further subdivided in nsplit_i x nsplit_j tiles. nsplit_i and nsplit_j are defined in run.def . nsplit_X needs not divide nbp exactly.

To run DYNAMICO on a parallel machine, you must first compile it with OpenMPI and/or MPI. Then use mpirun or the equivalent command to run it.
There must be less MPIxOpenMP processes than the 10 x nsplit_i x nsplit_j tiles. There can be more tiles than processes, in which case each process will take care of several tiles.

[[Category:DYNAMICO]]

WhatisDYNAMICO

2022-05-13T13:47:03Z

Dubos :

The DYNAMICO project develops a new dynamical core for LMD-Z, the atmospheric general circulation model (GCM) part of IPSL-CM Earth System Model.
LMDZ6, the current version of [https://lmdz.lmd.jussieu.fr/ LMDZ], has a shallow-atmosphere, hydrostatic dynamical core. It is based on a latitude-longitude C-grid, a hybrid pressure-based terrain-following vertical coordinate, second-order enstrophy-conserving finite-difference discretization and positive-definite advection. Grid refinement is implemented as a continuous zoom via smooth grid stretching. An extensive package of physical paramererizations is coupled to the dynamical core. IPSL-CM is currently used to produce AR5 simulations. LMD-Z is also at the heart of GCMs of planetary atmospheres (Mars, Venus and Titan).

It is well-known that the latitude-longitude coordinates have a strong singularity at the poles which is undesirable in terms of both numerical stability and computational efficiency. Regular tesselations of the sphere such as a recursively subdivided icosahedron provide an almost-uniform grid and a path to highly parallel computations based on domain decomposition. LMD's logo is itself an icosahedron, evoking the pioneering work of Robert Sadourny on the use of icosahedral grids for solving the equations of atmospheric motion.

The main role of DYNAMICO is to re-formulate in LMD-Z the horizontal advection and dynamics on a icosahedral grid, while preserving or improving their qualities with respect to accuracy, conservation laws and wave dispersion. Efficient implementation on present and future supercomputing architectures is also a key issue addressed by DYNAMICO.

DYNAMICO is currently able to solve the hydrostatic primitive equations and participated to the DCMIP workshop held in August 2012 at NCAR. In the near future we will investigate its extension to deep-atmosphere and possibly non-hydrostatic equations following a variational approach that naturally conserves mass, energy and, in a somewhat restricted sense, potential vorticity.

A grid refinement strategy based on variable-resolution, fully unstructured meshes is under development. A broader goal is to revisit all fundamental features of the dynamical core, especially the shallow-atmosphere/traditional approximation, the vertical coordinate and the coupling with physics.

[[Category:DYNAMICO]]

CompilingDYNAMICO

2022-05-13T13:42:09Z

Dubos : /* Compiling DYNAMICO */

= Getting and compiling DYNAMICO =

== Getting DYNAMICO ==
DYNAMICO is licensed under the [http://www.cecill.info/index.en.html CeCILL] open source license.
The latest version is accessible through git :
<pre>
git clone git@gitlab.in2p3.fr:ipsl/projets/dynamico/dynamico.git
git clone https://gitlab.in2p3.fr/ipsl/projets/dynamico/dynamico.git
</pre>

== Compiling DYNAMICO ==
DYNAMICO is written in Fortran 2003. The build process is based on [http://metomi.github.io/fcm/doc/user_guide/make.html FCM]. DYNAMICO requires the NetCDF library, including the F90 modules. MPI is required for parallel execution and XIOS for asynchronous I/O.

DYNAMICO depends on the NetCDF and BLAS/LAPACK libraries.

The compiling process is automated but some information is needed to guide it. This information is contained in text files in source:codes/icosagcm/trunk/arch . Sample files corresponding to a few machines (Ada at IDRIS, Curie at TGCC) are present. Assuming you compile on Ada :

<pre>
cd DYNAMICO
./make_icosa -arch X64_ADA -parallel mpi -prod -job 8
</pre>

will compile DYNAMICO. The make_icosa script accepts keyword-value pairs which drive its behaviour. The most important option is arch=ARCH (here ARCH=X64_ADA). It directs make_icosa to use the information contained in :
* arch/arch-ARCH.env
* arch/arch-ARCH.fcm
* arch/arch-ARCH.path

The *.env file is a shell script that is executed by make_icosa. It sets up the environment for use by *.path. *.path defines paths to libraries and modules needed for compilation. *.fcm defines the commands used to compile, link, etc. as well as options to be passed to the compiler/linker .

The option "-job 8" is similar to "make -j 8" and compiles in parallel for speed. After a successful build the main executable is found in the bin/ directory.

== Compiling with XIOS output ==
DYNAMICO can direct its output through XIOS, a parallel I/O library and server. See https://forge.ipsl.jussieu.fr/ioserver .
To enable XIOS output :
* get and compile XIOS in a separate directory
* set the variables XIOS_INCDIR , XIOS_LIBDIR and XIOS_LIB to appropriate values in your arch.path
* use the option "-with_xios" in your "make_icosa" command
Why use XIOS :
* without XIOS, each output field is written to a separate NetCDF file. Post-processing is required to group several fields together.
* with XIOS, several fields can be written to a few output files. This behavior is controlled by the input file xios.xml (required). See https://forge.ipsl.jussieu.fr/ioserver for the syntax of this XML file.
* without XIOS, data to be written is communicated to the main MPI process, which writes to the NetCDF files while other MPI processes stay idle. This is not expected to scale to a large number of MPI processes.
* XIOS provides asynchronous, parallel I/O in order to scale to large MPI process counts.

[[Category:DYNAMICO]]

CompilingDYNAMICO

2022-05-13T13:40:54Z

Dubos : Getting and compiling DYNAMICO

= Getting and compiling DYNAMICO =

== Getting DYNAMICO ==
DYNAMICO is licensed under the [http://www.cecill.info/index.en.html CeCILL] open source license.
The latest version is accessible through git :
<pre>
git clone git@gitlab.in2p3.fr:ipsl/projets/dynamico/dynamico.git
git clone https://gitlab.in2p3.fr/ipsl/projets/dynamico/dynamico.git
</pre>

== Compiling DYNAMICO ==
DYNAMICO is written in Fortran 90 with some legacy code in Fortran 77. The build process is based on [http://metomi.github.io/fcm/doc/user_guide/make.html FCM]. DYNAMICO requires the NetCDF library, including the F90 modules. MPI is required for parallel execution.

DYNAMICO depends on the NetCDF and BLAS/LAPACK libraries.

The compiling process is automated but some information is needed to guide it. This information is contained in text files in source:codes/icosagcm/trunk/arch . Sample files corresponding to a few machines (Ada at IDRIS, Curie at TGCC) are present. Assuming you compile on Ada :

<pre>
cd DYNAMICO
./make_icosa -arch X64_ADA -parallel mpi -prod -job 8
</pre>

will compile DYNAMICO. The make_icosa script accepts keyword-value pairs which drive its behaviour. The most important option is arch=ARCH (here ARCH=X64_ADA). It directs make_icosa to use the information contained in :
* arch/arch-ARCH.env
* arch/arch-ARCH.fcm
* arch/arch-ARCH.path

The *.env file is a shell script that is executed by make_icosa. It sets up the environment for use by *.path. *.path defines paths to libraries and modules needed for compilation. *.fcm defines the commands used to compile, link, etc. as well as options to be passed to the compiler/linker .

The option "-job 8" is similar to "make -j 8" and compiles in parallel for speed. After a successful build the main executable is found in the bin/ directory.

== Compiling with XIOS output ==
DYNAMICO can direct its output through XIOS, a parallel I/O library and server. See https://forge.ipsl.jussieu.fr/ioserver .
To enable XIOS output :
* get and compile XIOS in a separate directory
* set the variables XIOS_INCDIR , XIOS_LIBDIR and XIOS_LIB to appropriate values in your arch.path
* use the option "-with_xios" in your "make_icosa" command
Why use XIOS :
* without XIOS, each output field is written to a separate NetCDF file. Post-processing is required to group several fields together.
* with XIOS, several fields can be written to a few output files. This behavior is controlled by the input file xios.xml (required). See https://forge.ipsl.jussieu.fr/ioserver for the syntax of this XML file.
* without XIOS, data to be written is communicated to the main MPI process, which writes to the NetCDF files while other MPI processes stay idle. This is not expected to scale to a large number of MPI processes.
* XIOS provides asynchronous, parallel I/O in order to scale to large MPI process counts.

[[Category:DYNAMICO]]

CompilingDYNAMICO

2022-05-13T13:32:44Z

Dubos : Page créée avec « = Getting and compiling DYNAMICO = == Getting DYNAMICO == DYNAMICO is licensed under the [http://www.cecill.info/index.en.html CeCILL] open source license and should be c... »

= Getting and compiling DYNAMICO =

== Getting DYNAMICO ==
DYNAMICO is licensed under the [http://www.cecill.info/index.en.html CeCILL] open source license and should be considered beta-stage code.

The latest version is accessible through git :
<pre>
git clone git@gitlab.in2p3.fr:ipsl/projets/dynamico/dynamico.git
git clone https://gitlab.in2p3.fr/ipsl/projets/dynamico/dynamico.git
</pre>

== Compiling DYNAMICO ==
DYNAMICO is written in Fortran 90 with some legacy code in Fortran 77. The build process is based on [http://metomi.github.io/fcm/doc/user_guide/make.html FCM]. DYNAMICO requires the NetCDF library, including the F90 modules. MPI is required for parallel execution.

DYNAMICO depends on the NetCDF and BLAS/LAPACK libraries.

The compiling process is automated but some information is needed to guide it. This information is contained in text files in source:codes/icosagcm/trunk/arch . Sample files corresponding to a few machines (Ada at IDRIS, Curie at TGCC) are present. Assuming you compile on Ada :

<pre>
cd DYNAMICO
./make_icosa -arch X64_ADA -parallel mpi -prod -job 8
</pre>

will compile DYNAMICO. The make_icosa script accepts keyword-value pairs which drive its behaviour. The most important option is arch=ARCH (here ARCH=X64_ADA). It directs make_icosa to use the information contained in :
* arch/arch-ARCH.env
* arch/arch-ARCH.fcm
* arch/arch-ARCH.path

The *.env file is a shell script that is executed by make_icosa. It sets up the environment for use by *.path. *.path defines paths to libraries and modules needed for compilation. *.fcm defines the commands used to compile, link, etc. as well as options to be passed to the compiler/linker .

The option "-job 8" is similar to "make -j 8" and compiles in parallel for speed. After a successful build the main executable is found in the bin/ directory.

== Compiling with XIOS output ==
DYNAMICO can direct its output through XIOS, a parallel I/O library and server. See https://forge.ipsl.jussieu.fr/ioserver .
To enable XIOS output :
* get and compile XIOS in a separate directory
* set the variables XIOS_INCDIR , XIOS_LIBDIR and XIOS_LIB to appropriate values in your arch.path
* use the option "-with_xios" in your "make_icosa" command
Why use XIOS :
* without XIOS, each output field is written to a separate NetCDF file. Post-processing is required to group several fields together.
* with XIOS, several fields can be written to a few output files. This behavior is controlled by the input file xios.xml (required). See https://forge.ipsl.jussieu.fr/ioserver for the syntax of this XML file.
* without XIOS, data to be written is communicated to the main MPI process, which writes to the NetCDF files while other MPI processes stay idle. This is not expected to scale to a large number of MPI processes.
* XIOS provides asynchronous, parallel I/O in order to scale to large MPI process counts.

[[Category:DYNAMICO]]

Catégorie:DYNAMICO

2022-05-13T13:14:57Z

Dubos : Page créée avec « The DYNAMICO dynamical core. »

The DYNAMICO dynamical core.

WhatisDYNAMICO

2022-05-13T13:13:37Z

Dubos :

WhatisDYNAMICO

2022-05-13T13:12:31Z

Dubos : Page créée avec « The DYNAMICO project develops a new dynamical core for LMD-Z, the atmospheric general circulation model (GCM) part of IPSL-CM Earth System Model. LMDZ6, the current versio... »