Planets - User contributions [en]

Using Adastra

2023-06-15T08:24:29Z

Evos:

This page provides a summary of examples and tools designed to help you get used with the Adastra environment.

== Getting access to the cluster ==
For people on the "Atmosphères Planétaires" GENCI project who need to open an account on Adastra, here is the procedure:

# Go to https://www.edari.fr/utilisateur and log in via Janus or create an account if you don't have a Janus login. If this doesn't work, you can create a new eDARI account. (Make sure your profile is fully up to date including nationality)
# Click on "se rattacher à un dossier ayant obtenu des resources" or "Attach yourself to an application file that has obtained resources"
# "Atmosphères Planétaires" project number to provide: A0140110391
# Ehouarn then receives an email to allow you to join the project. Once he has validated it, you receive a confirmation mail.
# Once approved, you have to request for an account, click on "CINES: créer une demande d'ouverture de compte"
# fill in the forms: name, contract end date, CINES, your lab information (LMD is the default)
# Access IP address 134.157.47.46 , FQDN (Fully Qualified Domain Name): ssh-out.lmd.jussieu.fr
# Add a second adress : 134.157.176.129 , FQDN: ciclad.ipsl.upmc.fr
# click on option to have access to CCFR (only important if you have access to other GENCI machines)
# Security officer is Julien Lenseigne for LMD (his informations are all pre-filled, except phone: +33169335172)
# YOU MUST THEN VALIDATE THE REQUEST: click on the "Valider la saisie des informations"
# You then receive an automatic mail, but it's only to tell you to go to the next step: You must now download the pre-filled form from e-dari: find "télécharger la demande" and download the pdf. Sign it, and upload it on e-dari "déposer la demande de création de compte".
# Wait for your application to be preprocessed by the system...

== A couple of pointers ==

* Connecting to Adastra: For those who had an account on Occigen, we have retained group and login credentials from then; To connect to Adastra you need first go through the LMD gateway (hakim) or the IPSL (Ciclad/Spirit) gateway and then
<syntaxhighlight lang="bash">
ssh your_cines_login@adastra.cines.fr
</syntaxhighlight>
And then you will probably want to switch project using the myproject command, e.g. to switch to "lmd1167" (the old "Atmosphères Planétaires" GENCI project)
<syntaxhighlight lang="bash">
myproject -a lmd1167
</syntaxhighlight>
and to switch to "cin0391" (the 2023-2024 "Atmosphères Planétaires" GENCI project)
<syntaxhighlight lang="bash">
myproject -a cin0391
</syntaxhighlight>
WARNING: when you switch projects, you also switch HOME directory etc.

To get all the info about dedicated environment variables (e.g. paths to SCRATCH, STORE, etc.) you can use
<syntaxhighlight lang="bash">
myproject -c
</syntaxhighlight>

* Changing the password of your CINES account
When your password is close to expiring, CINES asks you to change it on this website : https://rosetta.cines.fr

Please note that you can access this website only if you are on a machine that you declared as a gateway for Adastra. At LMD, we have generally declared hakim.lmd.jussieu.fr (aka ssh-out) and ciclad.ipsl.jussieu.fr as gateway machines. Hakim doesn't have any browser installed, but you can launch <code>firefox</code> on Ciclad and connect to the rosetta website.
If that doesn't work, you will have to mail svp@cines.fr

* Link to the Adastra technical documentation: https://dci.dci-gitlab.cines.fr/webextranet/

== Submitting jobs ==
It's done using SLURM; you need to write up a job script and submit it using '''sbatch'''
<syntaxhighlight lang="bash">
sbatch myjob
</syntaxhighlight>
You must specify in the header of the job which project ressources you are using ("cin0391" in our case):
<syntaxhighlight lang="bash">
#SBATCH --account=cin0391
</syntaxhighlight>

=== Example of an MPI job to launch a simulation ===
<syntaxhighlight lang="bash">
#!/bin/bash
#SBATCH --job-name=job_mpi
#SBATCH --account=cin0391
### GENOA nodes accommodate 96 cores
#SBATCH --constraint=GENOA
### Number of Nodes to use
#SBATCH --nodes=1
### Number of MPI tasks per node
#SBATCH --ntasks-per-node=48
### Number of OpenMP threads per MPI task
#SBATCH --cpus-per-task=1
#SBATCH --threads-per-core=1
###SBATCH --exclusive
#SBATCH --output=job_mpi_%A.out
#SBATCH --time=00:45:00

#source env modules:
source ../trunk/LMDZ.COMMON/arch.env
ulimit -s unlimited

srun --cpu-bind=threads --label gcm_96x96x78_phyvenus_para.e > gcm.out 2>&1

</syntaxhighlight>

=== Example of a mixed MPI/OpenMP job to launch a simulation ===
<syntaxhighlight lang="bash">
#!/bin/bash
#SBATCH --job-name=job_mpi_omp
#SBATCH --account=cin0391
### GENOA nodes accommodate 96 cores
#SBATCH --constraint=GENOA
### Number of Nodes to use
#SBATCH --nodes=1
### Number of MPI tasks per node
#SBATCH --ntasks-per-node=24
### Number of OpenMP threads per MPI task
#SBATCH --cpus-per-task=4
#SBATCH --threads-per-core=1
###SBATCH --exclusive
#SBATCH --output=job_mpi_omp_%A.out
#SBATCH --time=00:30:00

#source env modules:
source ../trunk/LMDZ.COMMON/arch.env
ulimit -s unlimited

### OMP_NUM_THREADS value must match "#SBATCH --cpus-per-task"
export OMP_NUM_THREADS=4
export OMP_STACKSIZE=400M

srun --cpu-bind=threads --label gcm_64x48x54_phymars_para.e > gcm.out 2>&1

</syntaxhighlight>

[[Category:FAQ]]

Using Adastra

2023-06-15T07:16:12Z

Evos:

This page provides a summary of examples and tools designed to help you get used with the Adastra environment.

== Getting access to the cluster ==
For people on the "Atmosphères Planétaires" GENCI project who need to open an account on Adastra, here is the procedure:

# Go to https://www.edari.fr/utilisateur and log in via Janus or create an account if you don't have a Janus login. If this doesn't work, you can create a new eDARI account.
# Click on "se rattacher à un dossier ayant obtenu des resources" or "Attach yourself to an application file that has obtained resources"
# "Atmosphères Planétaires" project number to provide: A0140110391
# Ehouarn then receives an email to allow you to join the project. Once he has validated it, you receive a confirmation mail.
# Once approved, you have to request for an account, click on "CINES: créer une demande d'ouverture de compte"
# fill in the forms: name, contract end date, CINES, your lab information (LMD is the default)
# Access IP address 134.157.47.46 , FQDN (Fully Qualified Domain Name): ssh-out.lmd.jussieu.fr
# Add a second adress : 134.157.176.129 , FQDN: ciclad.ipsl.upmc.fr
# click on option to have access to CCFR (only important if you have access to other GENCI machines)
# Security officer is Julien Lenseigne for LMD (his informations are all pre-filled, except phone: +33169335172)
# YOU MUST THEN VALIDATE THE REQUEST: click on the "Valider la saisie des informations"
# You then receive an automatic mail, but it's only to tell you to go to the next step: You must now download the pre-filled form from e-dari: find "télécharger la demande" and download the pdf. Sign it, and upload it on e-dari "déposer la demande de création de compte".
# Wait for your application to be preprocessed by the system...

== A couple of pointers ==

* Connecting to Adastra: For those who had an account on Occigen, we have retained group and login credentials from then; To connect to Adastra you need first go through the LMD gateway (hakim) or the IPSL (Ciclad/Spirit) gateway and then
<syntaxhighlight lang="bash">
ssh your_cines_login@adastra.cines.fr
</syntaxhighlight>
And then you will probably want to switch project using the myproject command, e.g. to switch to "lmd1167" (the old "Atmosphères Planétaires" GENCI project)
<syntaxhighlight lang="bash">
myproject -a lmd1167
</syntaxhighlight>
and to switch to "cin0391" (the 2023-2024 "Atmosphères Planétaires" GENCI project)
<syntaxhighlight lang="bash">
myproject -a cin0391
</syntaxhighlight>
WARNING: when you switch projects, you also switch HOME directory etc.

To get all the info about dedicated environment variables (e.g. paths to SCRATCH, STORE, etc.) you can use
<syntaxhighlight lang="bash">
myproject -c
</syntaxhighlight>

* Changing the password of your CINES account
When your password is close to expiring, CINES asks you to change it on this website : https://rosetta.cines.fr

Please note that you can access this website only if you are on a machine that you declared as a gateway for Adastra. At LMD, we have generally declared hakim.lmd.jussieu.fr (aka ssh-out) and ciclad.ipsl.jussieu.fr as gateway machines. Hakim doesn't have any browser installed, but you can launch <code>firefox</code> on Ciclad and connect to the rosetta website.
If that doesn't work, you will have to mail svp@cines.fr

* Link to the Adastra technical documentation: https://dci.dci-gitlab.cines.fr/webextranet/

== Submitting jobs ==
It's done using SLURM; you need to write up a job script and submit it using '''sbatch'''
<syntaxhighlight lang="bash">
sbatch myjob
</syntaxhighlight>
You must specify in the header of the job which project ressources you are using ("cin0391" in our case):
<syntaxhighlight lang="bash">
#SBATCH --account=cin0391
</syntaxhighlight>

=== Example of an MPI job to launch a simulation ===
<syntaxhighlight lang="bash">
#!/bin/bash
#SBATCH --job-name=job_mpi
#SBATCH --account=cin0391
### GENOA nodes accommodate 96 cores
#SBATCH --constraint=GENOA
### Number of Nodes to use
#SBATCH --nodes=1
### Number of MPI tasks per node
#SBATCH --ntasks-per-node=48
### Number of OpenMP threads per MPI task
#SBATCH --cpus-per-task=1
#SBATCH --threads-per-core=1
###SBATCH --exclusive
#SBATCH --output=job_mpi_%A.out
#SBATCH --time=00:45:00

#source env modules:
source ../trunk/LMDZ.COMMON/arch.env
ulimit -s unlimited

srun --cpu-bind=threads --label gcm_96x96x78_phyvenus_para.e > gcm.out 2>&1

</syntaxhighlight>

=== Example of a mixed MPI/OpenMP job to launch a simulation ===
<syntaxhighlight lang="bash">
#!/bin/bash
#SBATCH --job-name=job_mpi_omp
#SBATCH --account=cin0391
### GENOA nodes accommodate 96 cores
#SBATCH --constraint=GENOA
### Number of Nodes to use
#SBATCH --nodes=1
### Number of MPI tasks per node
#SBATCH --ntasks-per-node=24
### Number of OpenMP threads per MPI task
#SBATCH --cpus-per-task=4
#SBATCH --threads-per-core=1
###SBATCH --exclusive
#SBATCH --output=job_mpi_omp_%A.out
#SBATCH --time=00:30:00

#source env modules:
source ../trunk/LMDZ.COMMON/arch.env
ulimit -s unlimited

### OMP_NUM_THREADS value must match "#SBATCH --cpus-per-task"
export OMP_NUM_THREADS=4
export OMP_STACKSIZE=400M

srun --cpu-bind=threads --label gcm_64x48x54_phymars_para.e > gcm.out 2>&1

</syntaxhighlight>

[[Category:FAQ]]

Using Adastra

2023-06-15T07:14:08Z

Evos:

This page provides a summary of examples and tools designed to help you get used with the Adastra environment.

== Getting access to the cluster ==
For people on the "Atmosphères Planétaires" GENCI project who need to open an account on Adastra, here is the procedure:

# Go to https://www.edari.fr/utilisateur and log in via Janus or create an account if you don't have a Janus login. If this doesn't work, you can create a new eDARI account.
# Click on "se rattacher à un dossier ayant obtenu des ressources"
# "Atmosphères Planétaires" project number to provide: A0140110391
# Ehouarn then receives an email to allow you to join the project. Once he has validated it, you receive a confirmation mail.
# Once approved, you have to request for an account, click on "CINES: créer une demande d'ouverture de compte"
# fill in the forms: name, contract end date, CINES, your lab information (LMD is the default)
# Access IP address 134.157.47.46 , FQDN (Fully Qualified Domain Name): ssh-out.lmd.jussieu.fr
# Add a second adress : 134.157.176.129 , FQDN: ciclad.ipsl.upmc.fr
# click on option to have access to CCFR (only important if you have access to other GENCI machines)
# Security officer is Julien Lenseigne for LMD (his informations are all pre-filled, except phone: +33169335172)
# YOU MUST THEN VALIDATE THE REQUEST: click on the "Valider la saisie des informations"
# You then receive an automatic mail, but it's only to tell you to go to the next step: You must now download the pre-filled form from e-dari: find "télécharger la demande" and download the pdf. Sign it, and upload it on e-dari "déposer la demande de création de compte".
# Wait for your application to be preprocessed by the system...

== A couple of pointers ==

* Connecting to Adastra: For those who had an account on Occigen, we have retained group and login credentials from then; To connect to Adastra you need first go through the LMD gateway (hakim) or the IPSL (Ciclad/Spirit) gateway and then
<syntaxhighlight lang="bash">
ssh your_cines_login@adastra.cines.fr
</syntaxhighlight>
And then you will probably want to switch project using the myproject command, e.g. to switch to "lmd1167" (the old "Atmosphères Planétaires" GENCI project)
<syntaxhighlight lang="bash">
myproject -a lmd1167
</syntaxhighlight>
and to switch to "cin0391" (the 2023-2024 "Atmosphères Planétaires" GENCI project)
<syntaxhighlight lang="bash">
myproject -a cin0391
</syntaxhighlight>
WARNING: when you switch projects, you also switch HOME directory etc.

To get all the info about dedicated environment variables (e.g. paths to SCRATCH, STORE, etc.) you can use
<syntaxhighlight lang="bash">
myproject -c
</syntaxhighlight>

* Changing the password of your CINES account
When your password is close to expiring, CINES asks you to change it on this website : https://rosetta.cines.fr

Please note that you can access this website only if you are on a machine that you declared as a gateway for Adastra. At LMD, we have generally declared hakim.lmd.jussieu.fr (aka ssh-out) and ciclad.ipsl.jussieu.fr as gateway machines. Hakim doesn't have any browser installed, but you can launch <code>firefox</code> on Ciclad and connect to the rosetta website.
If that doesn't work, you will have to mail svp@cines.fr

* Link to the Adastra technical documentation: https://dci.dci-gitlab.cines.fr/webextranet/

== Submitting jobs ==
It's done using SLURM; you need to write up a job script and submit it using '''sbatch'''
<syntaxhighlight lang="bash">
sbatch myjob
</syntaxhighlight>
You must specify in the header of the job which project ressources you are using ("cin0391" in our case):
<syntaxhighlight lang="bash">
#SBATCH --account=cin0391
</syntaxhighlight>

=== Example of an MPI job to launch a simulation ===
<syntaxhighlight lang="bash">
#!/bin/bash
#SBATCH --job-name=job_mpi
#SBATCH --account=cin0391
### GENOA nodes accommodate 96 cores
#SBATCH --constraint=GENOA
### Number of Nodes to use
#SBATCH --nodes=1
### Number of MPI tasks per node
#SBATCH --ntasks-per-node=48
### Number of OpenMP threads per MPI task
#SBATCH --cpus-per-task=1
#SBATCH --threads-per-core=1
###SBATCH --exclusive
#SBATCH --output=job_mpi_%A.out
#SBATCH --time=00:45:00

#source env modules:
source ../trunk/LMDZ.COMMON/arch.env
ulimit -s unlimited

srun --cpu-bind=threads --label gcm_96x96x78_phyvenus_para.e > gcm.out 2>&1

</syntaxhighlight>

=== Example of a mixed MPI/OpenMP job to launch a simulation ===
<syntaxhighlight lang="bash">
#!/bin/bash
#SBATCH --job-name=job_mpi_omp
#SBATCH --account=cin0391
### GENOA nodes accommodate 96 cores
#SBATCH --constraint=GENOA
### Number of Nodes to use
#SBATCH --nodes=1
### Number of MPI tasks per node
#SBATCH --ntasks-per-node=24
### Number of OpenMP threads per MPI task
#SBATCH --cpus-per-task=4
#SBATCH --threads-per-core=1
###SBATCH --exclusive
#SBATCH --output=job_mpi_omp_%A.out
#SBATCH --time=00:30:00

#source env modules:
source ../trunk/LMDZ.COMMON/arch.env
ulimit -s unlimited

### OMP_NUM_THREADS value must match "#SBATCH --cpus-per-task"
export OMP_NUM_THREADS=4
export OMP_STACKSIZE=400M

srun --cpu-bind=threads --label gcm_64x48x54_phymars_para.e > gcm.out 2>&1

</syntaxhighlight>

[[Category:FAQ]]

Mars Dynamico Installation manual

2023-06-13T13:20:37Z

Evos:

This page follows a manual for installing Mars Dynamico

1. Install the LMDZ Mars GCM and newstart
a) make sure u have the datafir and all of the *.def files.
b) create start.nc and startfi.nc
2. Compile start2archive_SSO
a) run : makelmdz_fcm -arch <archive> -d <dimensions (lonxlatxalt)> -p mars start2archive_SSO to create start_archive
b) run strart2archice_SSO
c) cp start_archive.nc to the dynamico_runs folder
3. Install Dynamico
a) use the following link to access the wiki page of Dynamico https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/The_DYNAMICO_dynamical_core
b) git clone https://gitlab.in2p3.fr/ipsl/projets/dynamico/dynamico.git
c) install XIOS, follow this link to access the wiki page of XIOS
1. if the make_xios dont work try this : ./make_xios --prod --arch ifort_MESOIPSL --arch_path ../ARCH --job 8 --full
d) move back to dynamico folder and run ./make_icosa -parallel <parralel_component> -with_xios -arch <archive> -job 8
if it doesnt work again add the arch path to ../ARCH
4. Create an initial condiations files for dynamico by running a dynamico simulation without the physics.
a) Compile make_icosa_lmdz in trunk/ICOSA_LMDZ
b) Copy from icosa_lmdz/bin/icosa_lmdz.exe to a dynamico_runs folder
c) Copy the xml files and the start files and the def files in the dynamico_runs directory and have access to the datadir.
input file start_archive.nc need be converted to NetCDF4 format
nccopy -k 4 start_archive.nc start_archive_nc4.nc
5. run dynamic.
a) In run_icosa.def change to run_length=1500, etat_isothermal_temp=200, etat=isothermal and startphy_file=false(not start_file)
b) copy datadir to the running directory
c) run icosa_lmdz.exe
d) copy the files outputed by icosa_lmdz.exe
1. cp restartfi.nc startphy_icosa_ref.nc
2. cp restart_icosa.nc start_icosa_ref.nc
6. move to LMDZ.mars/util/startarchive2icosa then change compile script to adapt for the right location of XIOS and run compile u should get start_archive2icosa and rearrange_startphy
a) copy start_archive2icosa and rearrange_startphy to the dynamico_runs folder.
b) Create surface_nc4.nc and copy it dynamico_runs folder
c) source arch.env
d) run ./start_archive2icosa as a job (requires a lot of memory) and make sure that Iodef.xml is the one for compile.
e) the script create start_icosa_prefinalize.nc and startfi_prefinalize.nc
f) copy icosa_finalize script form /trunk/LMDZ.MARS/util/startarchive2icosa/icosa_finalize.bash to dynamico_runs folder
g) change the XIOS and the for startfi0.nc paths in icosa_finalize.bash and run it. It adds and changes variables in the startfiles.
h) The scripts outputs startfi.nc and start_icosa.nc

7. update the tracer name in startfi for each tracer for example: ncrename -v ccn_number_surf,ccn_number startfi.nc

8. Run Dynamico simulation
a) change the iodef.xml
b) change in run_icosa.def etat0=start_file and add etat0_start_file_colocated=true

[[Category:Mars-DYNAMICO]]

Mars Dynamico Installation manual

2023-05-30T15:55:34Z

Evos:

This page follows a manual for installing Mars Dynamico

1. Install the LMDZ Mars GCM and newstart
a) make sure u have the datafir and all of the *.def files.
b) create start.nc and startfi.nc
2. Compile start2archive_SSO
a) run : makelmdz_fcm -arch <archive> -d <dimensions (lonxlatxalt)> -p mars start2archive_SSO to create start_archive
b) run strart2archice_SSO
c) cp start_archive.nc to the dynamico_runs folder
3. Install Dynamico
a) use the following link to access the wiki page of Dynamico https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/The_DYNAMICO_dynamical_core
b) git clone https://gitlab.in2p3.fr/ipsl/projets/dynamico/dynamico.git
c) install XIOS, follow this link to access the wiki page of XIOS
1. if the make_xios dont work try this : ./make_xios --prod --arch ifort_MESOIPSL --arch_path ../ARCH --job 8 --full
d) move back to dynamico folder and run ./make_icosa -parallel <parralel_component> -with_xios -arch <archive> -job 8
if it doesnt work again add the arch path to ../ARCH
4. Create an initial condiations files for dynamico by running a dynamico simulation without the physics.
a) Compile make_icosa_lmdz in trunk/ICOSA_LMDZ
b) Copy from icosa_lmdz/bin/icosa_lmdz.exe to a dynamico_runs folder
c) Copy the xml files and the start files and the def files in the dynamico_runs directory and have access to the datadir.
variable "nivsigs" needs be renamed "sigs" (XIOS requires CF-compliant files) (RV: No neeeded anymore)
ncrename -vnivsigs,sigs start_archive.nc
input file start_archive.nc need be converted to NetCDF4 format
nccopy -k 4 start_archive.nc start_archive_nc4.nc
5. run dynamic.
a) In run_icosa.def change to run_length=1500, etat_isothermal_temp=200, etat=isothermal and startphy_file=false(not start_file)
b) copy datadir to the running directory
c) run icosa_lmdz.exe
d) copy the files outputed by icosa_lmdz.exe
1. cp restartfi.nc startphy_icosa_ref.nc
2. cp restart_icosa.nc start_icosa_ref.nc
6. move to LMDZ.mars/util/startarchive2icosa then change compile script to adapt for the right location of XIOS and run compile u should get start_archive2icosa and rearrange_startphy
a) copy start_archive2icosa and rearrange_startphy to the dynamico_runs folder.
b) Create surface_nc4.nc and copy it dynamico_runs folder
c) source arch.env
d) run ./start_archive2icosa as a job (requires a lot of memory) and make sure that Iodef.xml is the one for compile.
e) the script create start_icosa_prefinalize.nc and startfi_prefinalize.nc
f) copy icosa_finalize script form /trunk/LMDZ.MARS/util/startarchive2icosa/icosa_finalize.bash to dynamico_runs folder
g) change the XIOS and the for startfi0.nc paths in icosa_finalize.bash and run it. It adds and changes variables in the startfiles.
h) The scripts outputs startfi.nc and start_icosa.nc

7. update the tracer name in startfi for each tracer for example: ncrename -v ccn_number_surf,ccn_number startfi.nc

8. Run Dynamico simulation
a) change the iodef.xml
b) change in run_icosa.def etat0=start_file and add etat0_start_file_colocated=true

[[Category:Mars-DYNAMICO]]

Mars Dynamico Installation manual

2023-05-30T15:03:18Z

Evos:

This page follows a manual for installing Mars Dynamico

1. Install the LMDZ Mars GCM and newstart
a) make sure u have the datafir and all of the *.def files.
b) create start.nc and startfi.nc
2. Compile start2archive_SSO
a) run : makelmdz_fcm -arch <archive> -d <dimensions (lonxlatxalt)> -p mars start2archive_SSO to create start_archive
b) run strart2archice_SSO
c) cp start_archive.nc to the dynamico_runs folder
3. Install Dynamico
a) use the following link to access the wiki page of Dynamico https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/The_DYNAMICO_dynamical_core
b) git clone https://gitlab.in2p3.fr/ipsl/projets/dynamico/dynamico.git
c) install XIOS, follow this link to access the wiki page of XIOS
1. if the make_xios dont work try this : ./make_xios --prod --arch ifort_MESOIPSL --arch_path ../ARCH --job 8 --full
d) move back to dynamico folder and run ./make_icosa -parallel <parralel_component> -with_xios -arch <archive> -job 8
if it doesnt work again add the arch path to ../ARCH
4. Create an initial condiations files for dynamico by running a dynamico simulation without the physics.
a) Compile make_icosa_lmdz in trunk/ICOSA_LMDZ
b) Copy from icosa_lmdz/bin/icosa_lmdz.exe to a dynamico_runs folder
c) Copy the xml files and the start files and the def files in the dynamico_runs directory and have access to the datadir.
variable "nivsigs" needs be renamed "sigs" (XIOS requires CF-compliant files) (RV: No neeeded anymore)
ncrename -vnivsigs,sigs start_archive.nc
input file start_archive.nc need be converted to NetCDF4 format
nccopy -k 4 start_archive.nc start_archive_nc4.nc
5. run dynamic.
a) In run_icosa.def change to run_length=1500, etat_isothermal_temp=200, etat=isothermal and startphy_file=false(not start_file)
b) copy datadir to the running directory
c) run icosa_lmdz.exe
d) copy the files outputed by icosa_lmdz.exe
1. cp restartfi.nc startphy_icosa_ref.nc
2. cp restart_icosa.nc start_icosa_ref.nc
6. move to LMDZ.mars/util/startarchive2icosa then change compile script to adapt for the right location of XIOS and run compile u should get start_archive2icosa and rearrange_startphy
a) copy start_archive2icosa and rearrange_startphy to the dynamico_runs folder.
b) Create surface_nc4.nc and copy it dynamico_runs folder
c) source arch.env
d) run ./start_archive2icosa as a job (requires a lot of memory) and make sure that Iodef.xml is the one for compile.
e) the script create start_icosa_prefinalize.nc and startfi_prefinalize.nc
f) copy icosa_finalize script form /trunk/LMDZ.MARS/util/startarchive2icosa/icosa_finalize.bash to dynamico_runs folder
g) change the XIOS and the for startfi0.nc paths in icosa_finalize.bash and run it. It adds and changes variables in the startfiles.
h) The scripts outputs startfi.nc and start_icosa.nc
i) In the current version of Dynamico, the variable q for tracer is needed but unused. To create this unused variable simply run this short python code
1. go into python
2. import numpy as np
3. import netCDF4 as nc
4. fn = 'start_icosa.nc'
5. ds = nc.Dataset(fn, 'a', format='NETCDF4')
6. nq = ds.createDimension('nq', 7)
7. q = ds.createVariable('q', 'f8', ('nq','lev', 'cell_mesh',))
8. nqq = ds.createVariable('nq', 'f8', ('nq',))
9. q[:,:,:]=0.
10. q.online_operation = "once"
11. q.coordinates = "lat lon"
12. ds.close()
7. update the tracer name in startfi for each tracer for example: ncrename -v ccn_number_surf,ccn_number startfi.nc

8. Run Dynamico simulation
a) change the iodef.xml
b) change in run_icosa.def etat0=start_file and add etat0_start_file_colocated=true
c) *sometimes weird variables can be missing like W and geopot : ncks -A -v geopot restart_icosa.nc start_icosa.nc

[[Category:Mars-DYNAMICO]]

Mars Dynamico Installation manual

2023-05-01T08:44:03Z

Evos: Created page with "This page follows a manual for installing Mars Dynamico 1. Install the LMDZ Mars GCM and newstart a) make sure u have the datafir and all of the *.def files. b) create..."

This page follows a manual for installing Mars Dynamico

1. Install the LMDZ Mars GCM and newstart
a) make sure u have the datafir and all of the *.def files.
b) create start.nc and startfi.nc
2. Compile start2archive_SSO
a) run : makelmdz_fcm -arch <archive> -d <dimensions (lonxlatxalt)> -p mars start2archive_SSO to create start_archive
b) run strart2archice_SSO
c) cp start_archive.nc to the dynamico_runs folder
3. Install Dynamico
a) use the following link to access the wiki page of Dynamico https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/The_DYNAMICO_dynamical_core
b) git clone https://gitlab.in2p3.fr/ipsl/projets/dynamico/dynamico.git
c) install XIOS, follow this link to access the wiki page of XIOS
1. if the make_xios dont work try this : ./make_xios --prod --arch ifort_MESOIPSL --arch_path ../ARCH --job 8 --full
d) move back to dynamico folder and run ./make_icosa -parallel <parralel_component> -with_xios -arch <archive> -job 8
if it doesnt work again add the arch path to ../ARCH
4. Create an initial condiations files for dynamico by running a dynamico simulation without the physics.
a) Compile make_icosa_lmdz in trunk/ICOSA_LMDZ
b) Copy from icosa_lmdz/bin/icosa_lmdz.exe to a dynamico_runs folder
c) Copy the xml files and the start files and the def files in the dynamico_runs directory and have access to the datadir.
variable "nivsigs" needs be renamed "sigs" (XIOS requires CF-compliant files) (RV: No neeeded anymore)
ncrename -vnivsigs,sigs start_archive.nc
input file start_archive.nc need be converted to NetCDF4 format
nccopy -k 4 start_archive.nc start_archive_nc4.nc
5. run dynamic.
a) In run_icosa.def change to run_length=1500, etat_isothermal_temp=200, etat=isothermal and startphy_file=false(not start_file)
b) copy datadir to the running directory
c) run icosa_lmdz.exe
d) copy the files outputed by icosa_lmdz.exe
1. cp restartfi.nc startphy_icosa_ref.nc
2. cp start_icosa0.nc start_icosa_ref.nc
6. move to LMDZ.mars/util/startarchive2icosa then change compile script to adapt for the right location of XIOS and run compile u should get start_archive2icosa and rearrange_startphy
a) copy start_archive2icosa and rearrange_startphy to the dynamico_runs folder.
b) Create surface_nc4.nc and copy it dynamico_runs folder
c) source arch.env
d) run ./start_archive2icosa as a job (requires a lot of memory) and make sure that Iodef.xml is the one for compile.
e) the script create start_icosa_prefinalize.nc and startfi_prefinalize.nc
f) copy icosa_finalize script form /trunk/LMDZ.MARS/util/startarchive2icosa/icosa_finalize.bash to dynamico_runs folder
g) change the XIOS and the for startfi0.nc paths in icosa_finalize.bash and run it. It adds and changes variables in the startfiles.
h) The scripts outputs startfi.nc and start_icosa.nc
i) In the current version of Dynamico, the variable q for tracer is needed but unused. To create this unused variable simply run this short python code
1. go into python
2. import numpy as np
3. import netCDF4 as nc
4. fn = 'start_icosa.nc'
5. ds = nc.Dataset(fn, 'a', format='NETCDF4')
6. nq = ds.createDimension('nq', 7)
7. q = ds.createVariable('q', 'f8', ('nq','lev', 'cell_mesh',))
8. nqq = ds.createVariable('nq', 'f8', ('nq',))
9. q[:,:,:]=0.
10. q.online_operation = "once"
11. q.coordinates = "lat lon"
12. ds.close()
7. update the tracer name in startfi for each tracer for example: ncrename -v ccn_number_surf,ccn_number startfi.nc

8. Run Dynamico simulation
a) change the iodef.xml
b) change in run_icosa.def etat0=start_file and add etat0_start_file_colocated=true
c) *sometimes weird variables can be missing like W and geopot : ncks -A -v geopot restart_icosa.nc start_icosa.nc

[[Category:Mars-DYNAMICO]]

1D PEM

2023-03-22T14:59:37Z

Evos:

1D PEM (under develpoment)

Run the 1D GCM for two years and then split the output to different years.
For example, I will take the output called diagfi.nc and will divide some variables (co2ice, h2o_ics_s ...) from it into 2 years.

ncks -v co2ice,h2o_ice_s,ps,tsurf -d Time,1,32111 diagfi.nc diagfi1.nc

ncks -v co2ice,h2o_ice_s,ps,tsurf -d Time,32112,64223 diagfi.nc diagfi2.nc

*Most of the physical variables in the 1D are stored in the def files so the PEM will update these files.

1D PEM

2023-03-22T13:33:30Z

Evos:

1D PEM

2023-03-22T13:33:14Z

Evos: Created page with "1D PEM (under develpoment) Run the 1D GCM for two years and then split the output to different years. For example, I will take the output called diagfi.nc and will divide so..."

1D PEM (under develpoment)

Run the 1D GCM for two years and then split the output to different years.
For example, I will take the output called diagfi.nc and will divide some variables (co2ice, h2o_ics_s ...) from it into 2 years.

ncks -v co2ice,h2o_ice_s,ps,tsurf -d Time,1,32111 diagfi.nc diagfi1.nc
ncks -v co2ice,h2o_ice_s,ps,tsurf -d Time,32112,64223 diagfi.nc diagfi2.nc

User:Evos

2023-03-22T13:29:50Z

Evos: Blanked the page

User:Evos

2023-03-22T13:28:44Z

Evos: 1D PEM (under develpoment)

1D PEM (under develpoment)

Run the 1D GCM for two years and then split the output to different years.
For example, I will take the output called diagfi.nc and will divide some variables (co2ice, h2o_ics_s ...) from it into 2 years.

ncks -v co2ice,h2o_ice_s,ps,tsurf -d Time,1,32111 diagfi.nc diagfi1.nc
ncks -v co2ice,h2o_ice_s,ps,tsurf -d Time,32112,64223 diagfi.nc diagfi2.nc