Wikicima - Contribuciones del usuario [es]

Página principal

2023-09-18T20:48:10Z

Lucia.cappelletti: /* Puntos clave a tener en cuenta para solicitar presupuesto y compra de pasaje vía el Programa OPTAR-FCEN */

== SCAD del CIMA (Cluster) ==
=== Reglamento de uso del SCAD del CIMA ===
Versión descargable: [[ Media:SCAD-Reglamento_de_uso.pdf‎ | SCAD-Reglamento_de_uso‎ ]]

==== General ====

*El siguiente reglamento puede ser modificado sin previo aviso y es responsabilidad de los usuarios mantenerse informados leyendo el mismo regularmente.

*El SCAD del CIMA sólo se puede utilizar para realizar corridas de procesos en paralelo con fines de investigación científica

*El SCAD es un recurso compartido por todos, por lo que debe usarse de forma RESPONSABLE y no se debe abusar del mismo

==== De su uso ====

*Está absolutamente prohibido navegar en internet o descargar archivos a través de los clusters. Sólo están permitidas las conexiones hacia los clusters a través de protocolos seguros (ssh, scp, etc.).

*La administración de las corridas (jobs) en los clusters se realiza a través de un sistema de colas (pbs). Esta prohibido lanzar corridas fuera del sistema de colas

*La cantidad de trabajos que pueden estar corriendo, depende de la cantidad y el tipo de nodos que hayan sido solicitados para cada una de las corridas.

*Sólo se puede utilizar para corridas de código paralelizado. Bajo ningún concepto se debe usar el nodo principal para correr programas seriales (Ej: pre y post procesamiento de los datos).

==== Almacenamiento ====

*Todos los archivos de salida deben ser almacenados en el directorio en el directorio de salidas de cada usuario ($HOME/salidas/). Los archivos pueden permanecer almacenados en este directorio durante un plazo máximo de 30 días al cabo de los cuales serán automáticamente eliminados.

*Cada usuario contará con un “$HOME” de poco tamaño para almacenar archivos permanentes (Ej: Programas, códigos, etc)

==== Agradecimiento ====

*Toda publicación que haya utilizado recursos del SCAD del CIMA debe contener el siguiente agradecimiento:
“Simulations were made with the high-performance computing clusters available at CIMA/UBA-CONICET, Argentina”

=== Autoridades ===
;Comité Asesor Científico:
: Claudio Menendez
: Juan Ruiz
: Celeste Saulo
: Silvina Solman
: Claudia Simionato (Directora CIMA)

;Coordinador:
: Juan Ruiz

;Supervisor:
: Gabriel Vieytes

=== Monitoreo ===

Página de monitoreo y estadísticas del SCAD del CIMA
*''''' http://scad.cima.fcen.uba.ar/

=== Solicitud de cuenta para uso del SCAD del CIMA ===
Para poder hacer uso de los cluster del SCAD del CIMA, es necesario solicitar la apertura de una cuenta personal enviando un mail a [mailto:soporte@cima.fcen.uba.ar soporte@cima.fcen.uba.ar].

=== Guía de usuario del SCAD del CIMA ===
Acceso a la Guía de usuario haciendo click [[Guía de usuario del SCAD del CIMA | aqui]]

=== Composición del SCAD del CIMA ===
Detalle de software y hardware que conforman el SCAD del cima haciendo click [[Composición del SCAD del CIMA | aqui ]]

=== Links ===
Links de referencia haciendo click [[Links | aqui ]]

=== FAQ ===
Preguntas frecuentes haciendo click [[FAQ | aqui ]]

== Datos ==


De los datos disponibles en el clúster SCAD (hydra) para simular (forzantes para modelos cómo el WRF, ORCHIDEE, ...) aquí [[DatosSCADSimular]]

Del grupo ILLAPA: 'Mecanismos del clima regional y sus impactos' descritos aquí [[DatosRCMSueloAtmosfera]]

== Reanalysis ==
'''Copia de los archivos para uso interno del CIMA'''. Datos Disponibles via FTP y DODS(**) de:
NCEP Climate Forecast System Reanalysis (CFSR)
ds093.0: 6-hourly Products / Reanalysis 1980-2010(*) / http://rda.ucar.edu/datasets/ds093.0/index.html

Para descargar los archivos via '''FTP''': ftp://usuario:password@datos.cima.fcen.uba.ar

Para abrir los archivos en forma remota '''DODS''': http://gds.cima.fcen.uba.ar:9090/dods/

'''Descripción y ayudas:''' http://www.cima.fcen.uba.ar/CFSR.html

'''Resolucion horizontal'''

Sudamerica: 0.5° x 0.5° - 15°N a 65°S y 30°W a 85°W ( 110 x 160 Longitud/Latitud)

Global: 2.5° x 2.5° - 90°N a 90°S y 0°E a 357.5°E ( 144 x 73 Longitud/Latitud)

'''Resolucion vertical''' en las variables de Nivel: 32 niveles de presión (mbar)

1000 975 950 925 900 875 850 825 800 775 750 700 650 600 550 500 450 400 350 300 250 225 200 175 150 125 100 70 50 30 20 10

'''Período''' 31 Años : 1980/01/01 a 2010/12/31

'''Frecuencia del Pronostico''': 0 6 12 18 h

'''25 VARIABLES DE SUPERFICIE'''

'''6 VARIABLES DE PRESION'''

== Modelos ==

*[[RCA]]

*[[WRF]]

*[[CESM]]

*[[MARS]]

*[[ORCHIDEE]]



== Documentación ==
*[[Redes avanzadas]]

*[[Libros]]

*[[Memoria Compartida (e.g.OpenMP)]]

*[[anaconda]]

*[[llaves ssh]]

*[[entornos python]]

*[[Configuración correo electrónico]]

*[[Configuración filtros webmail para avisos de vacaciones]]

*[[procesos zombies]]

*[[parTUXza]]

*[[Seguimiento simulaciones]]

*[[Spyder]]

*[[Jupyter Notebook]]

*[[Rstudio]]

*[[Cambio de contraseña]]

*[[VPN]]

* [[Café programación]]

== Reparaciones ==
*Documentación para ingreso de personal de service [[ Media:SEGUROS_CONTRAT_2016.pdf‎ | Seguros‎ ]]

*[[Empresas para service de AA]]

== Becarios ==

== Programa pasajes OPTAR-FCEN ==

==== General ====

En la Sub seccion '''Viajes''' de la Sección Trámites de la web oficial de la FCEN-UBA → https://exactas.uba.ar/ van a encontrar la Normativa vigente, el Instructivo y la Planilla de Solicitud del '''Programa Reserva y Pago de Pasajes Aéreos - Convenio FCEN-OPTAR'''

En el Instructivo van a encontrar QUÉ se debe hacer para que el uso del programa sea ''exitoso'', lo que viene a continuación son detalles clave a tener en cuenta pero no es la ''guía definitiva''.

Repito, LEAN EL INSTRUCTIVO PARA NO OLVIDAR PASOS CLAVE. E.g.: Una vez realizado el viaje el área requirente deberá enviar los pases de embarque correspondientes, a fin de que se pueda dar por realizado el viaje.

El programa puede ser utilizado tanto para que viaje gente de la FCEN como para que venga gente del extranjero a la FCEN -este último punto resulta clave por la evidente relación CIMA-Francia: para pasantías, para viajes de profesores invitades, autoridades IRD, etc.

==== Puntos clave a tener en cuenta para solicitar presupuesto y compra de pasaje vía el Programa OPTAR-FCEN ====

* la Planilla de Solicitud debe ser firmada por la Autoridad del Departamento, Instituto, Secretaria de quien viaja. En el caso del CIMA, la firma debe ser del Director del Instituto, en este caso el Prof. Pedro Flombaum

* la solicitud debe enviarse a hacienda@de.fcen.uba.ar, rosana@de.fcen.uba.ar, y a sicyt@de.fcen.uba.ar

* en el mail de solicitud debe ponerse en copia a la autoridad que firmó la planilla (en este caso el Prof. Flombaum)

* junto a la planilla completa con la firma de la autoridad debe adjuntarse una carta de invitación/aceptación -u otro documento- que avale la actividad que se llevará a cabo en el marco de la solicitud del pasaje

* en el cuerpo del correo se debe aclarar quién reintegrará el dinero a la facultad (la persona que viajará, el instituto al cual pertenece, institución que brinda becas, etc)

* el mail ''debería'' ser enviado desde la secretaría del instituto o departamento. En caso de que se tenga poco tiempo para hacer la solicitud, el correo lo puede enviar quien solicita presupuesto y posterior compra del pasaje, para que sea la primera persona en enterarse de las novedades

== Problemas habituales ==
* [[Phishing]]

== Compras ==
* [[Especificaciones servidor]]

Página principal

2023-09-18T20:43:11Z

Lucia.cappelletti: /* General */

== SCAD del CIMA (Cluster) ==
=== Reglamento de uso del SCAD del CIMA ===
Versión descargable: [[ Media:SCAD-Reglamento_de_uso.pdf‎ | SCAD-Reglamento_de_uso‎ ]]

==== General ====

*El siguiente reglamento puede ser modificado sin previo aviso y es responsabilidad de los usuarios mantenerse informados leyendo el mismo regularmente.

*El SCAD del CIMA sólo se puede utilizar para realizar corridas de procesos en paralelo con fines de investigación científica

*El SCAD es un recurso compartido por todos, por lo que debe usarse de forma RESPONSABLE y no se debe abusar del mismo

==== De su uso ====

*Está absolutamente prohibido navegar en internet o descargar archivos a través de los clusters. Sólo están permitidas las conexiones hacia los clusters a través de protocolos seguros (ssh, scp, etc.).

*La administración de las corridas (jobs) en los clusters se realiza a través de un sistema de colas (pbs). Esta prohibido lanzar corridas fuera del sistema de colas

*La cantidad de trabajos que pueden estar corriendo, depende de la cantidad y el tipo de nodos que hayan sido solicitados para cada una de las corridas.

*Sólo se puede utilizar para corridas de código paralelizado. Bajo ningún concepto se debe usar el nodo principal para correr programas seriales (Ej: pre y post procesamiento de los datos).

==== Almacenamiento ====

*Todos los archivos de salida deben ser almacenados en el directorio en el directorio de salidas de cada usuario ($HOME/salidas/). Los archivos pueden permanecer almacenados en este directorio durante un plazo máximo de 30 días al cabo de los cuales serán automáticamente eliminados.

*Cada usuario contará con un “$HOME” de poco tamaño para almacenar archivos permanentes (Ej: Programas, códigos, etc)

==== Agradecimiento ====

*Toda publicación que haya utilizado recursos del SCAD del CIMA debe contener el siguiente agradecimiento:
“Simulations were made with the high-performance computing clusters available at CIMA/UBA-CONICET, Argentina”

=== Autoridades ===
;Comité Asesor Científico:
: Claudio Menendez
: Juan Ruiz
: Celeste Saulo
: Silvina Solman
: Claudia Simionato (Directora CIMA)

;Coordinador:
: Juan Ruiz

;Supervisor:
: Gabriel Vieytes

=== Monitoreo ===

Página de monitoreo y estadísticas del SCAD del CIMA
*''''' http://scad.cima.fcen.uba.ar/

=== Solicitud de cuenta para uso del SCAD del CIMA ===
Para poder hacer uso de los cluster del SCAD del CIMA, es necesario solicitar la apertura de una cuenta personal enviando un mail a [mailto:soporte@cima.fcen.uba.ar soporte@cima.fcen.uba.ar].

=== Guía de usuario del SCAD del CIMA ===
Acceso a la Guía de usuario haciendo click [[Guía de usuario del SCAD del CIMA | aqui]]

=== Composición del SCAD del CIMA ===
Detalle de software y hardware que conforman el SCAD del cima haciendo click [[Composición del SCAD del CIMA | aqui ]]

=== Links ===
Links de referencia haciendo click [[Links | aqui ]]

=== FAQ ===
Preguntas frecuentes haciendo click [[FAQ | aqui ]]

== Datos ==


De los datos disponibles en el clúster SCAD (hydra) para simular (forzantes para modelos cómo el WRF, ORCHIDEE, ...) aquí [[DatosSCADSimular]]

Del grupo ILLAPA: 'Mecanismos del clima regional y sus impactos' descritos aquí [[DatosRCMSueloAtmosfera]]

== Reanalysis ==
'''Copia de los archivos para uso interno del CIMA'''. Datos Disponibles via FTP y DODS(**) de:
NCEP Climate Forecast System Reanalysis (CFSR)
ds093.0: 6-hourly Products / Reanalysis 1980-2010(*) / http://rda.ucar.edu/datasets/ds093.0/index.html

Para descargar los archivos via '''FTP''': ftp://usuario:password@datos.cima.fcen.uba.ar

Para abrir los archivos en forma remota '''DODS''': http://gds.cima.fcen.uba.ar:9090/dods/

'''Descripción y ayudas:''' http://www.cima.fcen.uba.ar/CFSR.html

'''Resolucion horizontal'''

Sudamerica: 0.5° x 0.5° - 15°N a 65°S y 30°W a 85°W ( 110 x 160 Longitud/Latitud)

Global: 2.5° x 2.5° - 90°N a 90°S y 0°E a 357.5°E ( 144 x 73 Longitud/Latitud)

'''Resolucion vertical''' en las variables de Nivel: 32 niveles de presión (mbar)

1000 975 950 925 900 875 850 825 800 775 750 700 650 600 550 500 450 400 350 300 250 225 200 175 150 125 100 70 50 30 20 10

'''Período''' 31 Años : 1980/01/01 a 2010/12/31

'''Frecuencia del Pronostico''': 0 6 12 18 h

'''25 VARIABLES DE SUPERFICIE'''

'''6 VARIABLES DE PRESION'''

== Modelos ==

*[[RCA]]

*[[WRF]]

*[[CESM]]

*[[MARS]]

*[[ORCHIDEE]]



== Documentación ==
*[[Redes avanzadas]]

*[[Libros]]

*[[Memoria Compartida (e.g.OpenMP)]]

*[[anaconda]]

*[[llaves ssh]]

*[[entornos python]]

*[[Configuración correo electrónico]]

*[[Configuración filtros webmail para avisos de vacaciones]]

*[[procesos zombies]]

*[[parTUXza]]

*[[Seguimiento simulaciones]]

*[[Spyder]]

*[[Jupyter Notebook]]

*[[Rstudio]]

*[[Cambio de contraseña]]

*[[VPN]]

* [[Café programación]]

== Reparaciones ==
*Documentación para ingreso de personal de service [[ Media:SEGUROS_CONTRAT_2016.pdf‎ | Seguros‎ ]]

*[[Empresas para service de AA]]

== Becarios ==

== Programa pasajes OPTAR-FCEN ==

==== General ====

En la Sub seccion '''Viajes''' de la Sección Trámites de la web oficial de la FCEN-UBA → https://exactas.uba.ar/ van a encontrar la Normativa vigente, el Instructivo y la Planilla de Solicitud del '''Programa Reserva y Pago de Pasajes Aéreos - Convenio FCEN-OPTAR'''

En el Instructivo van a encontrar QUÉ se debe hacer para que el uso del programa sea ''exitoso'', lo que viene a continuación son detalles clave a tener en cuenta pero no es la ''guía definitiva''.

Repito, LEAN EL INSTRUCTIVO PARA NO OLVIDAR PASOS CLAVE. E.g.: Una vez realizado el viaje el área requirente deberá enviar los pases de embarque correspondientes, a fin de que se pueda dar por realizado el viaje.

El programa puede ser utilizado tanto para que viaje gente de la FCEN como para que venga gente del extranjero a la FCEN -este último punto resulta clave por la evidente relación CIMA-Francia: para pasantías, para viajes de profesores invitades, autoridades IRD, etc.

==== Puntos clave a tener en cuenta para solicitar presupuesto y compra de pasaje vía el Programa OPTAR-FCEN ====

* la Planilla de Solicitud debe ser Firmada por la Autoridad del Departamento, Instituto, Secretaria de quien viaja. En el caso del CIMA, la firma debe ser del Director del Instituto, en este caso el Prof. Pedro Flombaum

* la solicitud debe enviarse a hacienda@de.fcen.uba.ar, rosana@de.fcen.uba.ar, y a sicyt@de.fcen.uba.ar

* en el mail de solicitud debe ponerse en copia a la autoridad que firmó la planilla (en este caso el Prof. Flombaum)

* junto a la planilla completa con la firma de la autoridad debe adjuntarse una carta de invitación/aceptación -u otro documento- que avale la actividad que se llevará a cabo en el marco de la solicitud de pasaje.

* en el cuerpo del correo se debe aclarar quién reintegrará el dinero a la facultad (la persona que viajará, el instituto al cual pertenece, institución que brinda becas, etc).

* el mail puede ser enviado desde la secretaría del instituto o departamento. En caso de que se tenga poco tiempo para hacer la solicitud, el correo lo puede enviar quien solicita presupuesto y posterior compra del pasaje, para que sea la primera persona en enterarse de las novedades.

== Problemas habituales ==
* [[Phishing]]

== Compras ==
* [[Especificaciones servidor]]

Página principal

2023-09-18T20:34:45Z

Lucia.cappelletti: /* Programa pasajes OPTAR-FCEN */

== SCAD del CIMA (Cluster) ==
=== Reglamento de uso del SCAD del CIMA ===
Versión descargable: [[ Media:SCAD-Reglamento_de_uso.pdf‎ | SCAD-Reglamento_de_uso‎ ]]

==== General ====

*El siguiente reglamento puede ser modificado sin previo aviso y es responsabilidad de los usuarios mantenerse informados leyendo el mismo regularmente.

*El SCAD del CIMA sólo se puede utilizar para realizar corridas de procesos en paralelo con fines de investigación científica

*El SCAD es un recurso compartido por todos, por lo que debe usarse de forma RESPONSABLE y no se debe abusar del mismo

==== De su uso ====

*Está absolutamente prohibido navegar en internet o descargar archivos a través de los clusters. Sólo están permitidas las conexiones hacia los clusters a través de protocolos seguros (ssh, scp, etc.).

*La administración de las corridas (jobs) en los clusters se realiza a través de un sistema de colas (pbs). Esta prohibido lanzar corridas fuera del sistema de colas

*La cantidad de trabajos que pueden estar corriendo, depende de la cantidad y el tipo de nodos que hayan sido solicitados para cada una de las corridas.

*Sólo se puede utilizar para corridas de código paralelizado. Bajo ningún concepto se debe usar el nodo principal para correr programas seriales (Ej: pre y post procesamiento de los datos).

==== Almacenamiento ====

*Todos los archivos de salida deben ser almacenados en el directorio en el directorio de salidas de cada usuario ($HOME/salidas/). Los archivos pueden permanecer almacenados en este directorio durante un plazo máximo de 30 días al cabo de los cuales serán automáticamente eliminados.

*Cada usuario contará con un “$HOME” de poco tamaño para almacenar archivos permanentes (Ej: Programas, códigos, etc)

==== Agradecimiento ====

*Toda publicación que haya utilizado recursos del SCAD del CIMA debe contener el siguiente agradecimiento:
“Simulations were made with the high-performance computing clusters available at CIMA/UBA-CONICET, Argentina”

=== Autoridades ===
;Comité Asesor Científico:
: Claudio Menendez
: Juan Ruiz
: Celeste Saulo
: Silvina Solman
: Claudia Simionato (Directora CIMA)

;Coordinador:
: Juan Ruiz

;Supervisor:
: Gabriel Vieytes

=== Monitoreo ===

Página de monitoreo y estadísticas del SCAD del CIMA
*''''' http://scad.cima.fcen.uba.ar/

=== Solicitud de cuenta para uso del SCAD del CIMA ===
Para poder hacer uso de los cluster del SCAD del CIMA, es necesario solicitar la apertura de una cuenta personal enviando un mail a [mailto:soporte@cima.fcen.uba.ar soporte@cima.fcen.uba.ar].

=== Guía de usuario del SCAD del CIMA ===
Acceso a la Guía de usuario haciendo click [[Guía de usuario del SCAD del CIMA | aqui]]

=== Composición del SCAD del CIMA ===
Detalle de software y hardware que conforman el SCAD del cima haciendo click [[Composición del SCAD del CIMA | aqui ]]

=== Links ===
Links de referencia haciendo click [[Links | aqui ]]

=== FAQ ===
Preguntas frecuentes haciendo click [[FAQ | aqui ]]

== Datos ==


De los datos disponibles en el clúster SCAD (hydra) para simular (forzantes para modelos cómo el WRF, ORCHIDEE, ...) aquí [[DatosSCADSimular]]

Del grupo ILLAPA: 'Mecanismos del clima regional y sus impactos' descritos aquí [[DatosRCMSueloAtmosfera]]

== Reanalysis ==
'''Copia de los archivos para uso interno del CIMA'''. Datos Disponibles via FTP y DODS(**) de:
NCEP Climate Forecast System Reanalysis (CFSR)
ds093.0: 6-hourly Products / Reanalysis 1980-2010(*) / http://rda.ucar.edu/datasets/ds093.0/index.html

Para descargar los archivos via '''FTP''': ftp://usuario:password@datos.cima.fcen.uba.ar

Para abrir los archivos en forma remota '''DODS''': http://gds.cima.fcen.uba.ar:9090/dods/

'''Descripción y ayudas:''' http://www.cima.fcen.uba.ar/CFSR.html

'''Resolucion horizontal'''

Sudamerica: 0.5° x 0.5° - 15°N a 65°S y 30°W a 85°W ( 110 x 160 Longitud/Latitud)

Global: 2.5° x 2.5° - 90°N a 90°S y 0°E a 357.5°E ( 144 x 73 Longitud/Latitud)

'''Resolucion vertical''' en las variables de Nivel: 32 niveles de presión (mbar)

1000 975 950 925 900 875 850 825 800 775 750 700 650 600 550 500 450 400 350 300 250 225 200 175 150 125 100 70 50 30 20 10

'''Período''' 31 Años : 1980/01/01 a 2010/12/31

'''Frecuencia del Pronostico''': 0 6 12 18 h

'''25 VARIABLES DE SUPERFICIE'''

'''6 VARIABLES DE PRESION'''

== Modelos ==

*[[RCA]]

*[[WRF]]

*[[CESM]]

*[[MARS]]

*[[ORCHIDEE]]



== Documentación ==
*[[Redes avanzadas]]

*[[Libros]]

*[[Memoria Compartida (e.g.OpenMP)]]

*[[anaconda]]

*[[llaves ssh]]

*[[entornos python]]

*[[Configuración correo electrónico]]

*[[Configuración filtros webmail para avisos de vacaciones]]

*[[procesos zombies]]

*[[parTUXza]]

*[[Seguimiento simulaciones]]

*[[Spyder]]

*[[Jupyter Notebook]]

*[[Rstudio]]

*[[Cambio de contraseña]]

*[[VPN]]

* [[Café programación]]

== Reparaciones ==
*Documentación para ingreso de personal de service [[ Media:SEGUROS_CONTRAT_2016.pdf‎ | Seguros‎ ]]

*[[Empresas para service de AA]]

== Becarios ==

== Programa pasajes OPTAR-FCEN ==

==== General ====

En la Sub seccion '''Viajes''' de la Sección Trámites de la web oficial de la FCEN-UBA → https://exactas.uba.ar/ van a encontrar la Normativa vigente, el Instructivo y la Planilla de Solicitud del '''Programa Reserva y Pago de Pasajes Aéreos - Convenio FCEN-OPTAR'''

En el Instructivo van a encontrar QUÉ se debe hacer para que el uso del programa sea ''exitoso'', lo que viene a continuación son detalles clave que deben tener en cuenta quienes quieras hacer uso de este programa.

Repito, LEAN EL INSTRUCTIVO PARA NO OLVIDAR PASOS CLAVE. E.g.: Una vez realizado el viaje el área requirente deberá enviar los pases de embarque correspondientes, a fin de que se pueda dar por realizado el viaje.

El programa puede ser utilizado tanto para que viaje gente de la FCEN como para que venga gente del extranjero a la FCEN -este último punto resulta clave por la evidente relación CIMA-Francia: para pasantías, para viajes de profesores invitades, autoridades IRD, etc.

==== Puntos clave a tener en cuenta para solicitar presupuesto y compra de pasaje vía el Programa OPTAR-FCEN ====

* la Planilla de Solicitud debe ser Firmada por la Autoridad del Departamento, Instituto, Secretaria de quien viaja. En el caso del CIMA, la firma debe ser del Director del Instituto, en este caso el Prof. Pedro Flombaum

* la solicitud debe enviarse a hacienda@de.fcen.uba.ar, rosana@de.fcen.uba.ar, y a sicyt@de.fcen.uba.ar

* en el mail de solicitud debe ponerse en copia a la autoridad que firmó la planilla (en este caso el Prof. Flombaum)

* junto a la planilla completa con la firma de la autoridad debe adjuntarse una carta de invitación/aceptación -u otro documento- que avale la actividad que se llevará a cabo en el marco de la solicitud de pasaje.

* en el cuerpo del correo se debe aclarar quién reintegrará el dinero a la facultad (la persona que viajará, el instituto al cual pertenece, institución que brinda becas, etc).

* el mail puede ser enviado desde la secretaría del instituto o departamento. En caso de que se tenga poco tiempo para hacer la solicitud, el correo lo puede enviar quien solicita presupuesto y posterior compra del pasaje, para que sea la primera persona en enterarse de las novedades.

== Problemas habituales ==
* [[Phishing]]

== Compras ==
* [[Especificaciones servidor]]

Página principal

2023-09-18T20:04:04Z

Lucia.cappelletti:

== SCAD del CIMA (Cluster) ==
=== Reglamento de uso del SCAD del CIMA ===
Versión descargable: [[ Media:SCAD-Reglamento_de_uso.pdf‎ | SCAD-Reglamento_de_uso‎ ]]

==== General ====

*El siguiente reglamento puede ser modificado sin previo aviso y es responsabilidad de los usuarios mantenerse informados leyendo el mismo regularmente.

*El SCAD del CIMA sólo se puede utilizar para realizar corridas de procesos en paralelo con fines de investigación científica

*El SCAD es un recurso compartido por todos, por lo que debe usarse de forma RESPONSABLE y no se debe abusar del mismo

==== De su uso ====

*Está absolutamente prohibido navegar en internet o descargar archivos a través de los clusters. Sólo están permitidas las conexiones hacia los clusters a través de protocolos seguros (ssh, scp, etc.).

*La administración de las corridas (jobs) en los clusters se realiza a través de un sistema de colas (pbs). Esta prohibido lanzar corridas fuera del sistema de colas

*La cantidad de trabajos que pueden estar corriendo, depende de la cantidad y el tipo de nodos que hayan sido solicitados para cada una de las corridas.

*Sólo se puede utilizar para corridas de código paralelizado. Bajo ningún concepto se debe usar el nodo principal para correr programas seriales (Ej: pre y post procesamiento de los datos).

==== Almacenamiento ====

*Todos los archivos de salida deben ser almacenados en el directorio en el directorio de salidas de cada usuario ($HOME/salidas/). Los archivos pueden permanecer almacenados en este directorio durante un plazo máximo de 30 días al cabo de los cuales serán automáticamente eliminados.

*Cada usuario contará con un “$HOME” de poco tamaño para almacenar archivos permanentes (Ej: Programas, códigos, etc)

==== Agradecimiento ====

*Toda publicación que haya utilizado recursos del SCAD del CIMA debe contener el siguiente agradecimiento:
“Simulations were made with the high-performance computing clusters available at CIMA/UBA-CONICET, Argentina”

=== Autoridades ===
;Comité Asesor Científico:
: Claudio Menendez
: Juan Ruiz
: Celeste Saulo
: Silvina Solman
: Claudia Simionato (Directora CIMA)

;Coordinador:
: Juan Ruiz

;Supervisor:
: Gabriel Vieytes

=== Monitoreo ===

Página de monitoreo y estadísticas del SCAD del CIMA
*''''' http://scad.cima.fcen.uba.ar/

=== Solicitud de cuenta para uso del SCAD del CIMA ===
Para poder hacer uso de los cluster del SCAD del CIMA, es necesario solicitar la apertura de una cuenta personal enviando un mail a [mailto:soporte@cima.fcen.uba.ar soporte@cima.fcen.uba.ar].

=== Guía de usuario del SCAD del CIMA ===
Acceso a la Guía de usuario haciendo click [[Guía de usuario del SCAD del CIMA | aqui]]

=== Composición del SCAD del CIMA ===
Detalle de software y hardware que conforman el SCAD del cima haciendo click [[Composición del SCAD del CIMA | aqui ]]

=== Links ===
Links de referencia haciendo click [[Links | aqui ]]

=== FAQ ===
Preguntas frecuentes haciendo click [[FAQ | aqui ]]

== Datos ==


De los datos disponibles en el clúster SCAD (hydra) para simular (forzantes para modelos cómo el WRF, ORCHIDEE, ...) aquí [[DatosSCADSimular]]

Del grupo ILLAPA: 'Mecanismos del clima regional y sus impactos' descritos aquí [[DatosRCMSueloAtmosfera]]

== Reanalysis ==
'''Copia de los archivos para uso interno del CIMA'''. Datos Disponibles via FTP y DODS(**) de:
NCEP Climate Forecast System Reanalysis (CFSR)
ds093.0: 6-hourly Products / Reanalysis 1980-2010(*) / http://rda.ucar.edu/datasets/ds093.0/index.html

Para descargar los archivos via '''FTP''': ftp://usuario:password@datos.cima.fcen.uba.ar

Para abrir los archivos en forma remota '''DODS''': http://gds.cima.fcen.uba.ar:9090/dods/

'''Descripción y ayudas:''' http://www.cima.fcen.uba.ar/CFSR.html

'''Resolucion horizontal'''

Sudamerica: 0.5° x 0.5° - 15°N a 65°S y 30°W a 85°W ( 110 x 160 Longitud/Latitud)

Global: 2.5° x 2.5° - 90°N a 90°S y 0°E a 357.5°E ( 144 x 73 Longitud/Latitud)

'''Resolucion vertical''' en las variables de Nivel: 32 niveles de presión (mbar)

1000 975 950 925 900 875 850 825 800 775 750 700 650 600 550 500 450 400 350 300 250 225 200 175 150 125 100 70 50 30 20 10

'''Período''' 31 Años : 1980/01/01 a 2010/12/31

'''Frecuencia del Pronostico''': 0 6 12 18 h

'''25 VARIABLES DE SUPERFICIE'''

'''6 VARIABLES DE PRESION'''

== Modelos ==

*[[RCA]]

*[[WRF]]

*[[CESM]]

*[[MARS]]

*[[ORCHIDEE]]



== Documentación ==
*[[Redes avanzadas]]

*[[Libros]]

*[[Memoria Compartida (e.g.OpenMP)]]

*[[anaconda]]

*[[llaves ssh]]

*[[entornos python]]

*[[Configuración correo electrónico]]

*[[Configuración filtros webmail para avisos de vacaciones]]

*[[procesos zombies]]

*[[parTUXza]]

*[[Seguimiento simulaciones]]

*[[Spyder]]

*[[Jupyter Notebook]]

*[[Rstudio]]

*[[Cambio de contraseña]]

*[[VPN]]

* [[Café programación]]

== Reparaciones ==
*Documentación para ingreso de personal de service [[ Media:SEGUROS_CONTRAT_2016.pdf‎ | Seguros‎ ]]

*[[Empresas para service de AA]]

== Becarios ==

== Programa pasajes OPTAR-FCEN ==

== Problemas habituales ==
* [[Phishing]]

== Compras ==
* [[Especificaciones servidor]]

ORCHIDEE

2023-03-07T13:42:01Z

Lucia.cappelletti: /* Running the model */

= ORCHIDEE =

This manual provides the information about the land-surface model [https://orchidee.ipsl.fr/ ORCHIDEE] (technical page for [http://forge.ipsl.jussieu.fr/orchidee advanced users]) from ''Institute Pierre Simone Laplace'' ([https://www.ipsl.fr/en IPSL]). Its installation on the HPC of the CIMA called <code>hydra</code>.

= Model description =

* ORCHIDEE: sechiba & stomate
* Two major modes of simulations: Off-line (no feedback) / on-line (LMDZ, WRF)

All forcing data to run ORCHIDEE is located here in CIMA's HPC:
<pre>
${ORforcing}=/share/DATA/ORCHIDEE/IGCM/
</pre>

== Off-line atmospheric forcings ==
Desdcribed here: [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/Forcings ORforcings]

Atmoshperic variables required by ORCHIDEE: <code>LWdown, PSurf, Qair, Rainf, SWdown, Snowf, Tair, Wind_E, Wind_N</code>

Available data-bases in hydra:
* WFDE5 CRU GPCC (v1, 0.5°): mixing ERA5 CRU and GPCC: <code>WFDE5_CRU_GPCC_[YYYY].nc</code> at <code>hydra</code>:
<pre>${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/</pre>

== Morphological forcings as data-base ==
Installed in CIMA's HPC hydra at
<pre>
/share/DATA/ORCHIDEE/IGCM/SRF
</pre>

To be interpolated to the domain of simulation (region and resolution) at the first time step (done by ORCHIDEE)
Mandatory:

=== PFT map ===

15 PFT, percentage of each by grid-point (<code>maxvegetfrac</code>, see table for equivalencies of PFT)

{| class="wikitable"
! num
! description
|-
| 1 || bare ground
|-
| 2 || tropical broad-leaved evergreen
|-
| 3 || tropical broad-leaved raingreen
|-
| 4 || temperate needleleaf evergreen
|-
| 5 || temperate broad-leaved evergreen
|-
| 6 || temperate broad-leaved summergreen
|-
| 7 || boreal needleleaf evergreen
|-
| 8 || boreal broad-leaved summergreen
|-
| 9 || boreal needleleaf summergreen
|-
| 10 || C3 grass
|-
| 11 || C4 grass
|-
| 12 || C3 agriculture
|-
| 13 || C4 agriculture
|-
| 14 || C3 tropical natural grassland
|-
| 15 || C4 boreal natural grassland
|}

<code>PFTmap_IPCC_[YYYY].nc</code> (0.5°, basic), a file per/year ESA-LUH2, v2 at:
<pre>${ORforcing}/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v2/PFTmap_2000.nc</pre>
<code>carteveg5km.nc</code> (Olson's global classification of 94 PFT, 5km transformation)

No temporal evolution at:
<pre>${ORforcing}/PFTMAPS/</pre>

[[File:Olson_vegetmap.png|frame|50px|Global Olson vegetation at 5 km of resolution Homolosine projection]]

=== Soil characterisitcs ===

* <code>soilcolor</code> used to define background-albedo: albedowet, albedodry (using values from 1 to 8). To be find in <code>soils_param.nc, soils_param_zobler.nc</code>
* <code>soiltexture</code> to define soil type, to be grouped as 3 types: corse, medium, fine (from 7 values). 3 different sources:
* <code>soils_param.nc</code> (1.°, basic)
* <code>soils_param_zobler.nc</code>: 7 types (1°)
* <code>soils_param_usda.nc</code>: 12 types (0.08331404°)

=== WOODHARVEST ===


=== SOIL_BULK ===


=== Additional ===
* LAI: on runs without <code>stomate</code> (otherwise, LAI is dynamic), one needs to provide climatologies of the LAI: 13 LAI values which evolves along time (monthly climatology) <code>lai2D_[00/01/03].nc</code>
* Albedo: on runs without <code>stomate</code> (otherwise, albedo is dynamic) new maps only for the bare soil albedo at higher resolution to avoid the use of <code>soilcolor</code> from <code>soils_param.nc</code>. Fixed values for wet/dry background albedo. Or a new file
** <code>alb_bg_jrctip.nc</code>: albedos climatologies retrieved from MODIS satellite JRC-TIP package
** <code>alb_bg_modisopt_2D.nc</code>: Another non.climatological albedo from MODIS
<pre>${ORforcing}/albedo</pre>
* Routing: <code>routing.nc</code>: worldwide data-base of river basins at 0.5°: 1-8 direction, <89 point at the sea, ... (<code>trip</code>), riverID (<code>basins</code>), water retention (<code>topoind</code>), etc..., <code>cartepente2d_15min.nc</code> topography slope (0.25°)
* Floodplains: <code>floodplain.nc</code> To account for maximum flooded area: <code>lake, dam, swamp, saline, pond, irrig</code>
* Chemistry: <code>orchidee_fertilizer_1995.nc</code> with fertilization (for N2) for rice and the others
* Reference Temperature: To be used as a reference temperature for the soil (<code>reftemp.nc</code>)

All ORCHIDEE configuration is controlled by <code>run.def</code>.: Domain, period, physics activation, sechiba/stomate, routing, floodplains, ... [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/OrchideeParameters ORparameters]

I/O controlled by <code>*.xml</code> files from [http://forge.ipsl.jussieu.fr/ioserver/ XIOS] libraries
* <code>iodef.xml</code>: main XIOS configuration
* <code>context_orchidee.xml</code>: I/O global configuration for ORCHIDEE
* <code>field_def_orchidee.xml</code>: definition of I/O variables (names, units, dimensions, long-name, ...)
* <code>file_def_orchidee.xml</code>: definition of variables at each file (output frequency, level of output, ...)

= Installation =
This installation guide is based on the installation in different machines from CIMA/DCAO computational resources:
* CIMA's HPC [[ORcompHYDRA hydra]]
* DCAO's computational classroom [[ORcompDCAO DCAO]]

which it must have pre-installed: netCDF libraries (netcdf-dev, netcdff), MPI libraries (mpi, mpich), Fortan and C compilers (gcc, gcc++ gfortran), pre-processing tools (cpp), subversion repository code tool (svn), Makefile (make, gmake), shells (ksh, csh)

''' NOTE '''
<pre>
Each new version of the code, has its own XIOS files! Make sure that you're using the right ones!! (otherwise, you would have an error...)
</pre>

= Running the model =
ORCHIDEE can run in a large variety of forms. Here is desribed a simple way to run a year of simulation using the off-line configuration and the trunk branch.

== Benchmark ==

Following this [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/TestCase1 instructions] we downloaded the necessary forcings in <code> /share/DATA/ORCHIDEE/benchmark </code>

== Test: let's look at Marcos Juárez, Córdoba, Argentina ==

Assuming a working directory <code>${WORKDIR}</code> (e.g.: <code>/home/lluis.fita/estudios/SensLuLc_MarcosJuarez/trunk</code>)

Writting of a simple <code>run.def</code> with stomate and routing activated for the 1980 year (the meaning and default values of all parameters are available [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/OrchideeParameters here]

<pre>
*****************************************************************************
START_DATE = 2001-01-01_00
END_DATE = 2001-12-31_00
TIME_LENGTH = 1Y
DT_SECHIBA = 900
#SPREAD_PREC_SEC = 3600 # The default is half the forcing time step
FORCING_FILE = forcing_yearm1.nc forcing_year.nc forcing_yearp1.nc

GRID_FILE = NONE
# South America
#LIMIT_WEST = -90.0
#LIMIT_EAST = -30.0
#LIMIT_SOUTH = -60.0
#LIMIT_NORTH = 15.0
# Marcos Juarez
LIMIT_WEST = -34.0
LIMIT_EAST = -30.0
LIMIT_SOUTH = -64.0
LIMIT_NORTH = -60.0
#*****************************************************************************

# Activate Stomate component (default y)
STOMATE_OK_STOMATE= y
STOMATE_OK_NCYCLE=FALSE

#
# Parameters related to the restart file and the start date
#**************************************************************************
# Time in the forcing file at which the model start if start date is not set by the forcing file (default 0)
TIME_SKIP = 0

# Time length for one intergration
# (default full lenght of forcing file)
#TIME_LENGTH = _AUTO_

# If DRIVER_reset_time=y, read the year from forcing file instead of taking it from restart file (default n)
#DRIVER_reset_time = _AUTO_

# Name of restart file for the driver (default NONE)
RESTART_FILEIN = NONE

# Name of restart file for sechiba part of the model (default NONE)
#SECHIBA_restart_in = _AUTOBLOCKER_

# Name of restart file for stomate part of the model (default NONE)
#STOMATE_RESTART_FILEIN = _AUTOBLOCKER_

# Parameters related to the diagnostic output files
#**************************************************************************
# Use XIOS for writing diagnostics file (default y)
XIOS_ORCHIDEE_OK = n

# Flag to activate sechiba_out_2.nc history file when using IOIPSL for SECHIBA (defulat n)
SECHIBA_HISTFILE2 = n

# Writefrequency in seconds in sechiba_history.nc when using IOIPSL (default 86400)
# If WRITE_STEP=0 then all IOIPSL output are deactivated
WRITE_STEP = 0

# Writefrequency in seconds sechiba_out_2.nc when using IOIPSL (default 1800)
WRITE_STEP2 = 0

# Writefrequency in days in stomate_history.nc when using IOIPSL (default 10)
STOMATE_HIST_DT = 0

# Writefrequency in days or -1 for monthly output in stomate_ipcc_history.nc when using IOIPSL (default 0)
STOMATE_IPCC_HIST_DT = 0

PRINTLEV=1000

# Hydrology parameters
#**************************************************************************
# Activate the multi-layer diffusion scheme adapted from CWRR (default y)
HYDROL_CWRR = y

# Activate river routing (default y)
RIVER_ROUTING = n
ROUTING_METHOD = highres
ROUTING_FILE = routing.nc
DT_ROUTING = 900
# Activate creation of river_desc.nc file
# RIVER_DESC will be activated only the first execution in the simulation
RIVER_DESC = y

# SOILTYPE_CLASSIF : Type of classification used for the map of soil types (default zobler)
SOILTYPE_CLASSIF = zobler

# Parameters related to vegetation map
#**************************************************************************
# Update vegetation frequency (default 0Y)
VEGET_UPDATE = 0Y

# Read lai map (default n)
LAI_MAP = n

# Prescribed vegetation (default n)
IMPOSE_VEG = n

# Parameters related to surface and thermal physical properties
#************************************************************************
# ROUGH_DYN : Account for a dynamic roughness height (activation of Su et al. parametrization) (default y)
ROUGH_DYN=y

# OK_FREEZE : Activate the complet soil freezing scheme (default y)
OK_FREEZE=y

# OK_EXPLICITSNOW : Activate explict snow scheme (default y)
OK_EXPLICITSNOW=y

# Carbon related parameters
#**************************************************************************
# Analytic spinup (default n)
SPINUP_ANALYTIC = n
SPINUP_PERIOD = n

# Value for atmospheric CO2 (default=350)
ATM_CO2 = 350

# Activate harvest of wood (default y)
DO_WOOD_HARVEST=y

# Deactivate fire (default FIRE_DISABLE=y)
FIRE_DISABLE=y

# Optimized parameters to be used with PFTmap with 15 pfts such as
# files in IGCM/SRF/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v1
#**************************************************************************
# Use 15 PFTs. Note that PFTmap.nc must contains 15PFTs.
# PFT=10, 14 and 15 share the same parametrization except for VCMAX25, LAI_MAX, FRAC_GROWTHRESP,
# MAINT_RESP_SLOPE_C and ALWAYS_INIT specified below.
# (default NVM=13)
NVM=15
PFT_TO_MTC=1,2,3,4,5,6,7,8,9,10,11,12,13,10,10
PFT_NAME__10='temperate C3 grass '
PFT_NAME__14='tropical C3 grass '
PFT_NAME__15='boreal C3 grass '

VCMAX25__10 = 50.0
VCMAX25__14 = 50.0
VCMAX25__15 = 40.0

LAI_MAX__10 = 2.5
LAI_MAX__14 = 2.5
LAI_MAX__15 = 2.0

FRAC_GROWTHRESP__10 = 0.28
FRAC_GROWTHRESP__14 = 0.35
FRAC_GROWTHRESP__15 = 0.35

MAINT_RESP_SLOPE_C__10 = 0.16
MAINT_RESP_SLOPE_C__14 = 0.12
MAINT_RESP_SLOPE_C__15 = 0.25

ALWAYS_INIT__10 = y
ALWAYS_INIT__14 = n
ALWAYS_INIT__15 = y
</pre>

Linking atomspheric forcing files (0.5° WFDE5 CRU GPCC v1 files)
<pre>
$ ln -s ${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_2000.nc ./forcing_yearm1.nc
$ ln -s ${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_2001.nc ./forcing_year.nc
$ ln -s ${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_2002.nc ./forcing_yearp1.nc
</pre>

Linking the routing data-base
<pre>$ ln -s ${ORforcing}/SRF/routing.nc ./</pre>

Linking the topographical slope
<pre>$ ln -s ${ORforcing}/SRF/cartepente2d_15min.nc ./</pre>

Linking the morphological files
<pre>$ ln -s ${ORforcing}/SRF/SOIL/soils_param_zobler.nc ./soils_param.nc
$ ln -s $ORforcing/SRF/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v2/PFTmap_1980.nc ./PFTmap.nc
</pre>

Getting the XIOS files (they might be version-dependant, therfore, it is recommended to get them directly from the same folder where the compiled version of ORCHIDEE is located, INSTALLDIR=/share/ORCHIDEE/)
<pre>$ cp $INSTALLDIR/modipsl/modeles/ORCHIDEE/src_xml/*xml ./</pre>

Edit the <code>file_def_orchidee.xml</code> to define output frequency and level of of output (remove all the <code>_AUTO_</code>)
<pre>$ vim file_def_orchidee.xml</pre>

The final configuration gets:
<pre>$ cat file_def_orchidee.xml | grep 'file id'
<file id="sechiba1" name="sechiba_history" output_level="11" output_freq="1d" enabled=".TRUE.">
<file id="sechiba2" name="sechiba_out_2" output_level="2" output_freq="1mo" enabled=".FALSE.">
<file id="sechiba3" name="sechiba_history_4dim" output_level="11" output_freq="1d" enabled=".TRUE.">
<file id="sechiba1_alma" name="sechiba_history_alma" output_level="10" output_freq="1mo" enabled=".FALSE.">
<file id="sechiba2_alma" name="sechiba_out_2_alma" output_level="10" output_freq="1d" enabled=".FALSE.">
<file id="sechiba4" name="sechiba_interp_diag" output_level="3" output_freq="1d" enabled=".TRUE.">
<file id="stomate1" name="stomate_history" output_level="10" output_freq="1d" enabled=".TRUE.">
<file id="stomate2" name="stomate_ipcc_history" output_level="1" output_freq="1mo" enabled=".FALSE.">
<file id="stomate3" name="stomate_history_4dim" output_level="11" output_freq="1d" enabled=".TRUE.">
<file id="stomate4" name="stomate_fixed_dia" output_level="4" output_freq="1" enabled=".FALSE.">
</pre>
Linking the ORCHIDEE executable
<pre>$ ln -s $INSTALLDIR/modipsl/bin/orchideedriver_prod ./orchideedriver
$ ln -s /share/ORCHIDEE/modipsl/bin/xios_server_prod.exe ./xios.exe
</pre>

Getting the PBS scheduling job to run ORCHIDEE
<pre>$ cp /share/ORCHIDEE/launch_orchidee.pbs ./</pre>

Launching the model
<pre>$ qsub launch_orchidee.pbs</pre>

There is a problem with the meteorological forcing data <code>IGCM/SRF/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_[nnnn].nc</code>, its time axis is units are: <code>'hours since 1900-01-01 00:00:00'</code>. But this gives an <code>IOIPSL</code> error from <code>flinopen_work</code> subroutine from <code>IOIPSL/src/flincom.f90</code> (lines #586-600):
<pre style="Fortran">
!---
!-- 5.1 Find the time axis. Prefered method is the 'timestep since'
!---
gdtmaf_id = -1
gdtt_id = -1
old_id = -1
DO iv=1,ncnbva(fid_out)
name=''
iret = NF90_INQUIRE_VARIABLE (fid, iv, name=name)
units=''
iret = NF90_GET_ATT (fid, iv, 'units', units)
IF (INDEX(units,'seconds since') > 0) gdtmaf_id = iv
IF (INDEX(units,'timesteps since') > 0) gdtt_id = iv
IF (INDEX(name, 'tstep') > 0 .OR. INDEX(name,'time') > 0 ) old_id = iv
ENDDO
</pre>
Therefore, axis time units have to changed to <code>'seconds since 1900-01-01 00:00:00'</code>


If everything went fine, one should have (at least)
<pre>orout/sechiba_history.nc orout/sechiba_history_4dim.nc stomate_history.nc</pre>
* <code>sechiba_history.nc</code>, <code>sechiba_history_4dim.nc</code>, <code>stomate_history.nc</code>: Outputs (optional, only when stomate is activated)
* <code>sechiba_rest_out.nc</code>, <code>stomate_restart.nc</code>: restarts for <code>sechiba<code> and <code>stomate</code> (optional, only when stomate is activated)
* <code>out_orchidee_[nnnn]</code>: standard output files for each process
* <code>river_desc.nc</code>: output with river description (optional, only when routing is activated)

== Running the model in DCAO's computational lab ==
Follow this link [[runORDCAO]] to set-up the runs in the machines of DCAO's computational laboratory

= OR4L: L. Fita's work-flow management for ORCHIDEE =
ORCHIDEE should be run with [http://forge.ipsl.jussieu.fr/libigcm libIGCM] which is a work-flow management for ORCHIDEE developed at the IPSL.

However, L. Fita developed an independent simpler and less potent work-flow called OR4L. See how it works in this wiki page [[ORCHIDEE/OR4L OR4L]]

= OR_1proc: DCAO's 1-proc work-flow management for ORCHIDEE =
DCAO's computational lab machines are 1 processors standard machines. A new work-flow management has been created for such cases. Mostly related to the UMI & DCAO course of [[http://www.cima.fcen.uba.ar/UMI/wrk/modelado-2019.php land-atmosphere interaction and its modelling]]. All the iformation is available in the wiki page [[OR1proc OR 1proc]]

ORCHIDEE

2023-03-07T13:36:05Z

Lucia.cappelletti: /* Benchmark */

ORCHIDEE

2023-03-07T13:34:08Z

Lucia.cappelletti: /* Benchmark */

= ORCHIDEE =

This manual provides the information about the land-surface model [https://orchidee.ipsl.fr/ ORCHIDEE] (technical page for [http://forge.ipsl.jussieu.fr/orchidee advanced users]) from ''Institute Pierre Simone Laplace'' ([https://www.ipsl.fr/en IPSL]). Its installation on the HPC of the CIMA called <code>hydra</code>.

= Model description =

* ORCHIDEE: sechiba & stomate
* Two major modes of simulations: Off-line (no feedback) / on-line (LMDZ, WRF)

All forcing data to run ORCHIDEE is located here in CIMA's HPC:
<pre>
${ORforcing}=/share/DATA/ORCHIDEE/IGCM/
</pre>

== Off-line atmospheric forcings ==
Desdcribed here: [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/Forcings ORforcings]

Atmoshperic variables required by ORCHIDEE: <code>LWdown, PSurf, Qair, Rainf, SWdown, Snowf, Tair, Wind_E, Wind_N</code>

Available data-bases in hydra:
* WFDE5 CRU GPCC (v1, 0.5°): mixing ERA5 CRU and GPCC: <code>WFDE5_CRU_GPCC_[YYYY].nc</code> at <code>hydra</code>:
<pre>${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/</pre>

== Morphological forcings as data-base ==
Installed in CIMA's HPC hydra at
<pre>
/share/DATA/ORCHIDEE/IGCM/SRF
</pre>

To be interpolated to the domain of simulation (region and resolution) at the first time step (done by ORCHIDEE)
Mandatory:

=== PFT map ===

15 PFT, percentage of each by grid-point (<code>maxvegetfrac</code>, see table for equivalencies of PFT)

{| class="wikitable"
! num
! description
|-
| 1 || bare ground
|-
| 2 || tropical broad-leaved evergreen
|-
| 3 || tropical broad-leaved raingreen
|-
| 4 || temperate needleleaf evergreen
|-
| 5 || temperate broad-leaved evergreen
|-
| 6 || temperate broad-leaved summergreen
|-
| 7 || boreal needleleaf evergreen
|-
| 8 || boreal broad-leaved summergreen
|-
| 9 || boreal needleleaf summergreen
|-
| 10 || C3 grass
|-
| 11 || C4 grass
|-
| 12 || C3 agriculture
|-
| 13 || C4 agriculture
|-
| 14 || C3 tropical natural grassland
|-
| 15 || C4 boreal natural grassland
|}

<code>PFTmap_IPCC_[YYYY].nc</code> (0.5°, basic), a file per/year ESA-LUH2, v2 at:
<pre>${ORforcing}/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v2/PFTmap_2000.nc</pre>
<code>carteveg5km.nc</code> (Olson's global classification of 94 PFT, 5km transformation)

No temporal evolution at:
<pre>${ORforcing}/PFTMAPS/</pre>

[[File:Olson_vegetmap.png|frame|50px|Global Olson vegetation at 5 km of resolution Homolosine projection]]

=== Soil characterisitcs ===

* <code>soilcolor</code> used to define background-albedo: albedowet, albedodry (using values from 1 to 8). To be find in <code>soils_param.nc, soils_param_zobler.nc</code>
* <code>soiltexture</code> to define soil type, to be grouped as 3 types: corse, medium, fine (from 7 values). 3 different sources:
* <code>soils_param.nc</code> (1.°, basic)
* <code>soils_param_zobler.nc</code>: 7 types (1°)
* <code>soils_param_usda.nc</code>: 12 types (0.08331404°)

=== WOODHARVEST ===


=== SOIL_BULK ===


=== Additional ===
* LAI: on runs without <code>stomate</code> (otherwise, LAI is dynamic), one needs to provide climatologies of the LAI: 13 LAI values which evolves along time (monthly climatology) <code>lai2D_[00/01/03].nc</code>
* Albedo: on runs without <code>stomate</code> (otherwise, albedo is dynamic) new maps only for the bare soil albedo at higher resolution to avoid the use of <code>soilcolor</code> from <code>soils_param.nc</code>. Fixed values for wet/dry background albedo. Or a new file
** <code>alb_bg_jrctip.nc</code>: albedos climatologies retrieved from MODIS satellite JRC-TIP package
** <code>alb_bg_modisopt_2D.nc</code>: Another non.climatological albedo from MODIS
<pre>${ORforcing}/albedo</pre>
* Routing: <code>routing.nc</code>: worldwide data-base of river basins at 0.5°: 1-8 direction, <89 point at the sea, ... (<code>trip</code>), riverID (<code>basins</code>), water retention (<code>topoind</code>), etc..., <code>cartepente2d_15min.nc</code> topography slope (0.25°)
* Floodplains: <code>floodplain.nc</code> To account for maximum flooded area: <code>lake, dam, swamp, saline, pond, irrig</code>
* Chemistry: <code>orchidee_fertilizer_1995.nc</code> with fertilization (for N2) for rice and the others
* Reference Temperature: To be used as a reference temperature for the soil (<code>reftemp.nc</code>)

All ORCHIDEE configuration is controlled by <code>run.def</code>.: Domain, period, physics activation, sechiba/stomate, routing, floodplains, ... [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/OrchideeParameters ORparameters]

I/O controlled by <code>*.xml</code> files from [http://forge.ipsl.jussieu.fr/ioserver/ XIOS] libraries
* <code>iodef.xml</code>: main XIOS configuration
* <code>context_orchidee.xml</code>: I/O global configuration for ORCHIDEE
* <code>field_def_orchidee.xml</code>: definition of I/O variables (names, units, dimensions, long-name, ...)
* <code>file_def_orchidee.xml</code>: definition of variables at each file (output frequency, level of output, ...)

= Installation =
This installation guide is based on the installation in different machines from CIMA/DCAO computational resources:
* CIMA's HPC [[ORcompHYDRA hydra]]
* DCAO's computational classroom [[ORcompDCAO DCAO]]

which it must have pre-installed: netCDF libraries (netcdf-dev, netcdff), MPI libraries (mpi, mpich), Fortan and C compilers (gcc, gcc++ gfortran), pre-processing tools (cpp), subversion repository code tool (svn), Makefile (make, gmake), shells (ksh, csh)

''' NOTE '''
<pre>
Each new version of the code, has its own XIOS files! Make sure that you're using the right ones!! (otherwise, you would have an error...)
</pre>

= Running the model =
ORCHIDEE can run in a large variety of forms. Here is desribed a simple way to run a year of simulation using the off-line configuration and the trunk branch.

== Benchmark ==

Following this [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/TestCase1 instructions] we downloaded the necessary forcings in <code> /share/DATA/ORCHIDEE/benchmark </code>

Assuming a working directory <code>${WORKDIR}</code> (e.g.: <code>/home/lluis.fita/estudios/SensLuLc_MarcosJuarez/trunk</code>)

Writting of a simple <code>run.def</code> with stomate and routing activated for the 1980 year (the meaning and default values of all parameters are available [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/OrchideeParameters here]

<pre>
*****************************************************************************
START_DATE = 2001-01-01_00
END_DATE = 2001-12-31_00
TIME_LENGTH = 1Y
DT_SECHIBA = 900
#SPREAD_PREC_SEC = 3600 # The default is half the forcing time step
FORCING_FILE = forcing_yearm1.nc forcing_year.nc forcing_yearp1.nc

GRID_FILE = NONE
# South America
#LIMIT_WEST = -90.0
#LIMIT_EAST = -30.0
#LIMIT_SOUTH = -60.0
#LIMIT_NORTH = 15.0
# Marcos Juarez
LIMIT_WEST = -34.0
LIMIT_EAST = -30.0
LIMIT_SOUTH = -64.0
LIMIT_NORTH = -60.0
#*****************************************************************************

# Activate Stomate component (default y)
STOMATE_OK_STOMATE= y
STOMATE_OK_NCYCLE=FALSE

#
# Parameters related to the restart file and the start date
#**************************************************************************
# Time in the forcing file at which the model start if start date is not set by the forcing file (default 0)
TIME_SKIP = 0

# Time length for one intergration
# (default full lenght of forcing file)
#TIME_LENGTH = _AUTO_

# If DRIVER_reset_time=y, read the year from forcing file instead of taking it from restart file (default n)
#DRIVER_reset_time = _AUTO_

# Name of restart file for the driver (default NONE)
RESTART_FILEIN = NONE

# Name of restart file for sechiba part of the model (default NONE)
#SECHIBA_restart_in = _AUTOBLOCKER_

# Name of restart file for stomate part of the model (default NONE)
#STOMATE_RESTART_FILEIN = _AUTOBLOCKER_

# Parameters related to the diagnostic output files
#**************************************************************************
# Use XIOS for writing diagnostics file (default y)
XIOS_ORCHIDEE_OK = n

# Flag to activate sechiba_out_2.nc history file when using IOIPSL for SECHIBA (defulat n)
SECHIBA_HISTFILE2 = n

# Writefrequency in seconds in sechiba_history.nc when using IOIPSL (default 86400)
# If WRITE_STEP=0 then all IOIPSL output are deactivated
WRITE_STEP = 0

# Writefrequency in seconds sechiba_out_2.nc when using IOIPSL (default 1800)
WRITE_STEP2 = 0

# Writefrequency in days in stomate_history.nc when using IOIPSL (default 10)
STOMATE_HIST_DT = 0

# Writefrequency in days or -1 for monthly output in stomate_ipcc_history.nc when using IOIPSL (default 0)
STOMATE_IPCC_HIST_DT = 0

PRINTLEV=1000

# Hydrology parameters
#**************************************************************************
# Activate the multi-layer diffusion scheme adapted from CWRR (default y)
HYDROL_CWRR = y

# Activate river routing (default y)
RIVER_ROUTING = n
ROUTING_METHOD = highres
ROUTING_FILE = routing.nc
DT_ROUTING = 900
# Activate creation of river_desc.nc file
# RIVER_DESC will be activated only the first execution in the simulation
RIVER_DESC = y

# SOILTYPE_CLASSIF : Type of classification used for the map of soil types (default zobler)
SOILTYPE_CLASSIF = zobler

# Parameters related to vegetation map
#**************************************************************************
# Update vegetation frequency (default 0Y)
VEGET_UPDATE = 0Y

# Read lai map (default n)
LAI_MAP = n

# Prescribed vegetation (default n)
IMPOSE_VEG = n

# Parameters related to surface and thermal physical properties
#************************************************************************
# ROUGH_DYN : Account for a dynamic roughness height (activation of Su et al. parametrization) (default y)
ROUGH_DYN=y

# OK_FREEZE : Activate the complet soil freezing scheme (default y)
OK_FREEZE=y

# OK_EXPLICITSNOW : Activate explict snow scheme (default y)
OK_EXPLICITSNOW=y

# Carbon related parameters
#**************************************************************************
# Analytic spinup (default n)
SPINUP_ANALYTIC = n
SPINUP_PERIOD = n

# Value for atmospheric CO2 (default=350)
ATM_CO2 = 350

# Activate harvest of wood (default y)
DO_WOOD_HARVEST=y

# Deactivate fire (default FIRE_DISABLE=y)
FIRE_DISABLE=y

# Optimized parameters to be used with PFTmap with 15 pfts such as
# files in IGCM/SRF/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v1
#**************************************************************************
# Use 15 PFTs. Note that PFTmap.nc must contains 15PFTs.
# PFT=10, 14 and 15 share the same parametrization except for VCMAX25, LAI_MAX, FRAC_GROWTHRESP,
# MAINT_RESP_SLOPE_C and ALWAYS_INIT specified below.
# (default NVM=13)
NVM=15
PFT_TO_MTC=1,2,3,4,5,6,7,8,9,10,11,12,13,10,10
PFT_NAME__10='temperate C3 grass '
PFT_NAME__14='tropical C3 grass '
PFT_NAME__15='boreal C3 grass '

VCMAX25__10 = 50.0
VCMAX25__14 = 50.0
VCMAX25__15 = 40.0

LAI_MAX__10 = 2.5
LAI_MAX__14 = 2.5
LAI_MAX__15 = 2.0

FRAC_GROWTHRESP__10 = 0.28
FRAC_GROWTHRESP__14 = 0.35
FRAC_GROWTHRESP__15 = 0.35

MAINT_RESP_SLOPE_C__10 = 0.16
MAINT_RESP_SLOPE_C__14 = 0.12
MAINT_RESP_SLOPE_C__15 = 0.25

ALWAYS_INIT__10 = y
ALWAYS_INIT__14 = n
ALWAYS_INIT__15 = y
</pre>

Linking atomspheric forcing files (0.5° WFDE5 CRU GPCC v1 files)
<pre>
$ ln -s ${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_2000.nc ./forcing_yearm1.nc
$ ln -s ${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_2001.nc ./forcing_year.nc
$ ln -s ${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_2002.nc ./forcing_yearp1.nc
</pre>

Linking the routing data-base
<pre>$ ln -s ${ORforcing}/SRF/routing.nc ./</pre>

Linking the topographical slope
<pre>$ ln -s ${ORforcing}/SRF/cartepente2d_15min.nc ./</pre>

Linking the morphological files
<pre>$ ln -s ${ORforcing}/SRF/SOIL/soils_param_zobler.nc ./soils_param.nc
$ ln -s $ORforcing/SRF/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v2/PFTmap_1980.nc ./PFTmap.nc
</pre>

Getting the XIOS files (they might be version-dependant, therfore, it is recommended to get them directly from the same folder where the compiled version of ORCHIDEE is located, INSTALLDIR=/share/ORCHIDEE/)
<pre>$ cp $INSTALLDIR/modipsl/modeles/ORCHIDEE/src_xml/*xml ./</pre>

Edit the <code>file_def_orchidee.xml</code> to define output frequency and level of of output (remove all the <code>_AUTO_</code>)
<pre>$ vim file_def_orchidee.xml</pre>

The final configuration gets:
<pre>$ cat file_def_orchidee.xml | grep 'file id'
<file id="sechiba1" name="sechiba_history" output_level="11" output_freq="1d" enabled=".TRUE.">
<file id="sechiba2" name="sechiba_out_2" output_level="2" output_freq="1mo" enabled=".FALSE.">
<file id="sechiba3" name="sechiba_history_4dim" output_level="11" output_freq="1d" enabled=".TRUE.">
<file id="sechiba1_alma" name="sechiba_history_alma" output_level="10" output_freq="1mo" enabled=".FALSE.">
<file id="sechiba2_alma" name="sechiba_out_2_alma" output_level="10" output_freq="1d" enabled=".FALSE.">
<file id="sechiba4" name="sechiba_interp_diag" output_level="3" output_freq="1d" enabled=".TRUE.">
<file id="stomate1" name="stomate_history" output_level="10" output_freq="1d" enabled=".TRUE.">
<file id="stomate2" name="stomate_ipcc_history" output_level="1" output_freq="1mo" enabled=".FALSE.">
<file id="stomate3" name="stomate_history_4dim" output_level="11" output_freq="1d" enabled=".TRUE.">
<file id="stomate4" name="stomate_fixed_dia" output_level="4" output_freq="1" enabled=".FALSE.">
</pre>
Linking the ORCHIDEE executable
<pre>$ ln -s $INSTALLDIR/modipsl/bin/orchideedriver_prod ./orchideedriver
$ ln -s /share/ORCHIDEE/modipsl/bin/xios_server_prod.exe ./xios.exe
</pre>

Getting the PBS scheduling job to run ORCHIDEE
<pre>$ cp /share/ORCHIDEE/launch_orchidee.pbs ./</pre>

Launching the model
<pre>$ qsub launch_orchidee.pbs</pre>

There is a problem with the meteorological forcing data <code>IGCM/SRF/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_[nnnn].nc</code>, its time axis is units are: <code>'hours since 1900-01-01 00:00:00'</code>. But this gives an <code>IOIPSL</code> error from <code>flinopen_work</code> subroutine from <code>IOIPSL/src/flincom.f90</code> (lines #586-600):
<pre style="Fortran">
!---
!-- 5.1 Find the time axis. Prefered method is the 'timestep since'
!---
gdtmaf_id = -1
gdtt_id = -1
old_id = -1
DO iv=1,ncnbva(fid_out)
name=''
iret = NF90_INQUIRE_VARIABLE (fid, iv, name=name)
units=''
iret = NF90_GET_ATT (fid, iv, 'units', units)
IF (INDEX(units,'seconds since') > 0) gdtmaf_id = iv
IF (INDEX(units,'timesteps since') > 0) gdtt_id = iv
IF (INDEX(name, 'tstep') > 0 .OR. INDEX(name,'time') > 0 ) old_id = iv
ENDDO
</pre>
Therefore, axis time units have to changed to <code>'seconds since 1900-01-01 00:00:00'</code>


If everything went fine, one should have (at least)
<pre>orout/sechiba_history.nc orout/sechiba_history_4dim.nc stomate_history.nc</pre>
* <code>sechiba_history.nc</code>, <code>sechiba_history_4dim.nc</code>, <code>stomate_history.nc</code>: Outputs (optional, only when stomate is activated)
* <code>sechiba_rest_out.nc</code>, <code>stomate_restart.nc</code>: restarts for <code>sechiba<code> and <code>stomate</code> (optional, only when stomate is activated)
* <code>out_orchidee_[nnnn]</code>: standard output files for each process
* <code>river_desc.nc</code>: output with river description (optional, only when routing is activated)

== Running the model in DCAO's computational lab ==
Follow this link [[runORDCAO]] to set-up the runs in the machines of DCAO's computational laboratory

= OR4L: L. Fita's work-flow management for ORCHIDEE =
ORCHIDEE should be run with [http://forge.ipsl.jussieu.fr/libigcm libIGCM] which is a work-flow management for ORCHIDEE developed at the IPSL.

However, L. Fita developed an independent simpler and less potent work-flow called OR4L. See how it works in this wiki page [[ORCHIDEE/OR4L OR4L]]

= OR_1proc: DCAO's 1-proc work-flow management for ORCHIDEE =
DCAO's computational lab machines are 1 processors standard machines. A new work-flow management has been created for such cases. Mostly related to the UMI & DCAO course of [[http://www.cima.fcen.uba.ar/UMI/wrk/modelado-2019.php land-atmosphere interaction and its modelling]]. All the iformation is available in the wiki page [[OR1proc OR 1proc]]

ORCHIDEE

2023-03-07T13:33:28Z

Lucia.cappelletti: /* Running the model */

= ORCHIDEE =

This manual provides the information about the land-surface model [https://orchidee.ipsl.fr/ ORCHIDEE] (technical page for [http://forge.ipsl.jussieu.fr/orchidee advanced users]) from ''Institute Pierre Simone Laplace'' ([https://www.ipsl.fr/en IPSL]). Its installation on the HPC of the CIMA called <code>hydra</code>.

= Model description =

* ORCHIDEE: sechiba & stomate
* Two major modes of simulations: Off-line (no feedback) / on-line (LMDZ, WRF)

All forcing data to run ORCHIDEE is located here in CIMA's HPC:
<pre>
${ORforcing}=/share/DATA/ORCHIDEE/IGCM/
</pre>

== Off-line atmospheric forcings ==
Desdcribed here: [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/Forcings ORforcings]

Atmoshperic variables required by ORCHIDEE: <code>LWdown, PSurf, Qair, Rainf, SWdown, Snowf, Tair, Wind_E, Wind_N</code>

Available data-bases in hydra:
* WFDE5 CRU GPCC (v1, 0.5°): mixing ERA5 CRU and GPCC: <code>WFDE5_CRU_GPCC_[YYYY].nc</code> at <code>hydra</code>:
<pre>${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/</pre>

== Morphological forcings as data-base ==
Installed in CIMA's HPC hydra at
<pre>
/share/DATA/ORCHIDEE/IGCM/SRF
</pre>

To be interpolated to the domain of simulation (region and resolution) at the first time step (done by ORCHIDEE)
Mandatory:

=== PFT map ===

15 PFT, percentage of each by grid-point (<code>maxvegetfrac</code>, see table for equivalencies of PFT)

{| class="wikitable"
! num
! description
|-
| 1 || bare ground
|-
| 2 || tropical broad-leaved evergreen
|-
| 3 || tropical broad-leaved raingreen
|-
| 4 || temperate needleleaf evergreen
|-
| 5 || temperate broad-leaved evergreen
|-
| 6 || temperate broad-leaved summergreen
|-
| 7 || boreal needleleaf evergreen
|-
| 8 || boreal broad-leaved summergreen
|-
| 9 || boreal needleleaf summergreen
|-
| 10 || C3 grass
|-
| 11 || C4 grass
|-
| 12 || C3 agriculture
|-
| 13 || C4 agriculture
|-
| 14 || C3 tropical natural grassland
|-
| 15 || C4 boreal natural grassland
|}

<code>PFTmap_IPCC_[YYYY].nc</code> (0.5°, basic), a file per/year ESA-LUH2, v2 at:
<pre>${ORforcing}/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v2/PFTmap_2000.nc</pre>
<code>carteveg5km.nc</code> (Olson's global classification of 94 PFT, 5km transformation)

No temporal evolution at:
<pre>${ORforcing}/PFTMAPS/</pre>

[[File:Olson_vegetmap.png|frame|50px|Global Olson vegetation at 5 km of resolution Homolosine projection]]

=== Soil characterisitcs ===

* <code>soilcolor</code> used to define background-albedo: albedowet, albedodry (using values from 1 to 8). To be find in <code>soils_param.nc, soils_param_zobler.nc</code>
* <code>soiltexture</code> to define soil type, to be grouped as 3 types: corse, medium, fine (from 7 values). 3 different sources:
* <code>soils_param.nc</code> (1.°, basic)
* <code>soils_param_zobler.nc</code>: 7 types (1°)
* <code>soils_param_usda.nc</code>: 12 types (0.08331404°)

=== WOODHARVEST ===


=== SOIL_BULK ===


=== Additional ===
* LAI: on runs without <code>stomate</code> (otherwise, LAI is dynamic), one needs to provide climatologies of the LAI: 13 LAI values which evolves along time (monthly climatology) <code>lai2D_[00/01/03].nc</code>
* Albedo: on runs without <code>stomate</code> (otherwise, albedo is dynamic) new maps only for the bare soil albedo at higher resolution to avoid the use of <code>soilcolor</code> from <code>soils_param.nc</code>. Fixed values for wet/dry background albedo. Or a new file
** <code>alb_bg_jrctip.nc</code>: albedos climatologies retrieved from MODIS satellite JRC-TIP package
** <code>alb_bg_modisopt_2D.nc</code>: Another non.climatological albedo from MODIS
<pre>${ORforcing}/albedo</pre>
* Routing: <code>routing.nc</code>: worldwide data-base of river basins at 0.5°: 1-8 direction, <89 point at the sea, ... (<code>trip</code>), riverID (<code>basins</code>), water retention (<code>topoind</code>), etc..., <code>cartepente2d_15min.nc</code> topography slope (0.25°)
* Floodplains: <code>floodplain.nc</code> To account for maximum flooded area: <code>lake, dam, swamp, saline, pond, irrig</code>
* Chemistry: <code>orchidee_fertilizer_1995.nc</code> with fertilization (for N2) for rice and the others
* Reference Temperature: To be used as a reference temperature for the soil (<code>reftemp.nc</code>)

All ORCHIDEE configuration is controlled by <code>run.def</code>.: Domain, period, physics activation, sechiba/stomate, routing, floodplains, ... [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/OrchideeParameters ORparameters]

I/O controlled by <code>*.xml</code> files from [http://forge.ipsl.jussieu.fr/ioserver/ XIOS] libraries
* <code>iodef.xml</code>: main XIOS configuration
* <code>context_orchidee.xml</code>: I/O global configuration for ORCHIDEE
* <code>field_def_orchidee.xml</code>: definition of I/O variables (names, units, dimensions, long-name, ...)
* <code>file_def_orchidee.xml</code>: definition of variables at each file (output frequency, level of output, ...)

= Installation =
This installation guide is based on the installation in different machines from CIMA/DCAO computational resources:
* CIMA's HPC [[ORcompHYDRA hydra]]
* DCAO's computational classroom [[ORcompDCAO DCAO]]

which it must have pre-installed: netCDF libraries (netcdf-dev, netcdff), MPI libraries (mpi, mpich), Fortan and C compilers (gcc, gcc++ gfortran), pre-processing tools (cpp), subversion repository code tool (svn), Makefile (make, gmake), shells (ksh, csh)

''' NOTE '''
<pre>
Each new version of the code, has its own XIOS files! Make sure that you're using the right ones!! (otherwise, you would have an error...)
</pre>

= Running the model =
ORCHIDEE can run in a large variety of forms. Here is desribed a simple way to run a year of simulation using the off-line configuration and the trunk branch.

== Benchmark ==

Following this [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/TestCase1 instructions] we downloaded the necessary forcings in <code>/share/DATA/ORCHIDEE/benchmark/<code>

Assuming a working directory <code>${WORKDIR}</code> (e.g.: <code>/home/lluis.fita/estudios/SensLuLc_MarcosJuarez/trunk</code>)

Writting of a simple <code>run.def</code> with stomate and routing activated for the 1980 year (the meaning and default values of all parameters are available [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/OrchideeParameters here]

<pre>
*****************************************************************************
START_DATE = 2001-01-01_00
END_DATE = 2001-12-31_00
TIME_LENGTH = 1Y
DT_SECHIBA = 900
#SPREAD_PREC_SEC = 3600 # The default is half the forcing time step
FORCING_FILE = forcing_yearm1.nc forcing_year.nc forcing_yearp1.nc

GRID_FILE = NONE
# South America
#LIMIT_WEST = -90.0
#LIMIT_EAST = -30.0
#LIMIT_SOUTH = -60.0
#LIMIT_NORTH = 15.0
# Marcos Juarez
LIMIT_WEST = -34.0
LIMIT_EAST = -30.0
LIMIT_SOUTH = -64.0
LIMIT_NORTH = -60.0
#*****************************************************************************

# Activate Stomate component (default y)
STOMATE_OK_STOMATE= y
STOMATE_OK_NCYCLE=FALSE

#
# Parameters related to the restart file and the start date
#**************************************************************************
# Time in the forcing file at which the model start if start date is not set by the forcing file (default 0)
TIME_SKIP = 0

# Time length for one intergration
# (default full lenght of forcing file)
#TIME_LENGTH = _AUTO_

# If DRIVER_reset_time=y, read the year from forcing file instead of taking it from restart file (default n)
#DRIVER_reset_time = _AUTO_

# Name of restart file for the driver (default NONE)
RESTART_FILEIN = NONE

# Name of restart file for sechiba part of the model (default NONE)
#SECHIBA_restart_in = _AUTOBLOCKER_

# Name of restart file for stomate part of the model (default NONE)
#STOMATE_RESTART_FILEIN = _AUTOBLOCKER_

# Parameters related to the diagnostic output files
#**************************************************************************
# Use XIOS for writing diagnostics file (default y)
XIOS_ORCHIDEE_OK = n

# Flag to activate sechiba_out_2.nc history file when using IOIPSL for SECHIBA (defulat n)
SECHIBA_HISTFILE2 = n

# Writefrequency in seconds in sechiba_history.nc when using IOIPSL (default 86400)
# If WRITE_STEP=0 then all IOIPSL output are deactivated
WRITE_STEP = 0

# Writefrequency in seconds sechiba_out_2.nc when using IOIPSL (default 1800)
WRITE_STEP2 = 0

# Writefrequency in days in stomate_history.nc when using IOIPSL (default 10)
STOMATE_HIST_DT = 0

# Writefrequency in days or -1 for monthly output in stomate_ipcc_history.nc when using IOIPSL (default 0)
STOMATE_IPCC_HIST_DT = 0

PRINTLEV=1000

# Hydrology parameters
#**************************************************************************
# Activate the multi-layer diffusion scheme adapted from CWRR (default y)
HYDROL_CWRR = y

# Activate river routing (default y)
RIVER_ROUTING = n
ROUTING_METHOD = highres
ROUTING_FILE = routing.nc
DT_ROUTING = 900
# Activate creation of river_desc.nc file
# RIVER_DESC will be activated only the first execution in the simulation
RIVER_DESC = y

# SOILTYPE_CLASSIF : Type of classification used for the map of soil types (default zobler)
SOILTYPE_CLASSIF = zobler

# Parameters related to vegetation map
#**************************************************************************
# Update vegetation frequency (default 0Y)
VEGET_UPDATE = 0Y

# Read lai map (default n)
LAI_MAP = n

# Prescribed vegetation (default n)
IMPOSE_VEG = n

# Parameters related to surface and thermal physical properties
#************************************************************************
# ROUGH_DYN : Account for a dynamic roughness height (activation of Su et al. parametrization) (default y)
ROUGH_DYN=y

# OK_FREEZE : Activate the complet soil freezing scheme (default y)
OK_FREEZE=y

# OK_EXPLICITSNOW : Activate explict snow scheme (default y)
OK_EXPLICITSNOW=y

# Carbon related parameters
#**************************************************************************
# Analytic spinup (default n)
SPINUP_ANALYTIC = n
SPINUP_PERIOD = n

# Value for atmospheric CO2 (default=350)
ATM_CO2 = 350

# Activate harvest of wood (default y)
DO_WOOD_HARVEST=y

# Deactivate fire (default FIRE_DISABLE=y)
FIRE_DISABLE=y

# Optimized parameters to be used with PFTmap with 15 pfts such as
# files in IGCM/SRF/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v1
#**************************************************************************
# Use 15 PFTs. Note that PFTmap.nc must contains 15PFTs.
# PFT=10, 14 and 15 share the same parametrization except for VCMAX25, LAI_MAX, FRAC_GROWTHRESP,
# MAINT_RESP_SLOPE_C and ALWAYS_INIT specified below.
# (default NVM=13)
NVM=15
PFT_TO_MTC=1,2,3,4,5,6,7,8,9,10,11,12,13,10,10
PFT_NAME__10='temperate C3 grass '
PFT_NAME__14='tropical C3 grass '
PFT_NAME__15='boreal C3 grass '

VCMAX25__10 = 50.0
VCMAX25__14 = 50.0
VCMAX25__15 = 40.0

LAI_MAX__10 = 2.5
LAI_MAX__14 = 2.5
LAI_MAX__15 = 2.0

FRAC_GROWTHRESP__10 = 0.28
FRAC_GROWTHRESP__14 = 0.35
FRAC_GROWTHRESP__15 = 0.35

MAINT_RESP_SLOPE_C__10 = 0.16
MAINT_RESP_SLOPE_C__14 = 0.12
MAINT_RESP_SLOPE_C__15 = 0.25

ALWAYS_INIT__10 = y
ALWAYS_INIT__14 = n
ALWAYS_INIT__15 = y
</pre>

Linking atomspheric forcing files (0.5° WFDE5 CRU GPCC v1 files)
<pre>
$ ln -s ${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_2000.nc ./forcing_yearm1.nc
$ ln -s ${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_2001.nc ./forcing_year.nc
$ ln -s ${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_2002.nc ./forcing_yearp1.nc
</pre>

Linking the routing data-base
<pre>$ ln -s ${ORforcing}/SRF/routing.nc ./</pre>

Linking the topographical slope
<pre>$ ln -s ${ORforcing}/SRF/cartepente2d_15min.nc ./</pre>

Linking the morphological files
<pre>$ ln -s ${ORforcing}/SRF/SOIL/soils_param_zobler.nc ./soils_param.nc
$ ln -s $ORforcing/SRF/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v2/PFTmap_1980.nc ./PFTmap.nc
</pre>

Getting the XIOS files (they might be version-dependant, therfore, it is recommended to get them directly from the same folder where the compiled version of ORCHIDEE is located, INSTALLDIR=/share/ORCHIDEE/)
<pre>$ cp $INSTALLDIR/modipsl/modeles/ORCHIDEE/src_xml/*xml ./</pre>

Edit the <code>file_def_orchidee.xml</code> to define output frequency and level of of output (remove all the <code>_AUTO_</code>)
<pre>$ vim file_def_orchidee.xml</pre>

The final configuration gets:
<pre>$ cat file_def_orchidee.xml | grep 'file id'
<file id="sechiba1" name="sechiba_history" output_level="11" output_freq="1d" enabled=".TRUE.">
<file id="sechiba2" name="sechiba_out_2" output_level="2" output_freq="1mo" enabled=".FALSE.">
<file id="sechiba3" name="sechiba_history_4dim" output_level="11" output_freq="1d" enabled=".TRUE.">
<file id="sechiba1_alma" name="sechiba_history_alma" output_level="10" output_freq="1mo" enabled=".FALSE.">
<file id="sechiba2_alma" name="sechiba_out_2_alma" output_level="10" output_freq="1d" enabled=".FALSE.">
<file id="sechiba4" name="sechiba_interp_diag" output_level="3" output_freq="1d" enabled=".TRUE.">
<file id="stomate1" name="stomate_history" output_level="10" output_freq="1d" enabled=".TRUE.">
<file id="stomate2" name="stomate_ipcc_history" output_level="1" output_freq="1mo" enabled=".FALSE.">
<file id="stomate3" name="stomate_history_4dim" output_level="11" output_freq="1d" enabled=".TRUE.">
<file id="stomate4" name="stomate_fixed_dia" output_level="4" output_freq="1" enabled=".FALSE.">
</pre>
Linking the ORCHIDEE executable
<pre>$ ln -s $INSTALLDIR/modipsl/bin/orchideedriver_prod ./orchideedriver
$ ln -s /share/ORCHIDEE/modipsl/bin/xios_server_prod.exe ./xios.exe
</pre>

Getting the PBS scheduling job to run ORCHIDEE
<pre>$ cp /share/ORCHIDEE/launch_orchidee.pbs ./</pre>

Launching the model
<pre>$ qsub launch_orchidee.pbs</pre>

There is a problem with the meteorological forcing data <code>IGCM/SRF/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_[nnnn].nc</code>, its time axis is units are: <code>'hours since 1900-01-01 00:00:00'</code>. But this gives an <code>IOIPSL</code> error from <code>flinopen_work</code> subroutine from <code>IOIPSL/src/flincom.f90</code> (lines #586-600):
<pre style="Fortran">
!---
!-- 5.1 Find the time axis. Prefered method is the 'timestep since'
!---
gdtmaf_id = -1
gdtt_id = -1
old_id = -1
DO iv=1,ncnbva(fid_out)
name=''
iret = NF90_INQUIRE_VARIABLE (fid, iv, name=name)
units=''
iret = NF90_GET_ATT (fid, iv, 'units', units)
IF (INDEX(units,'seconds since') > 0) gdtmaf_id = iv
IF (INDEX(units,'timesteps since') > 0) gdtt_id = iv
IF (INDEX(name, 'tstep') > 0 .OR. INDEX(name,'time') > 0 ) old_id = iv
ENDDO
</pre>
Therefore, axis time units have to changed to <code>'seconds since 1900-01-01 00:00:00'</code>


If everything went fine, one should have (at least)
<pre>orout/sechiba_history.nc orout/sechiba_history_4dim.nc stomate_history.nc</pre>
* <code>sechiba_history.nc</code>, <code>sechiba_history_4dim.nc</code>, <code>stomate_history.nc</code>: Outputs (optional, only when stomate is activated)
* <code>sechiba_rest_out.nc</code>, <code>stomate_restart.nc</code>: restarts for <code>sechiba<code> and <code>stomate</code> (optional, only when stomate is activated)
* <code>out_orchidee_[nnnn]</code>: standard output files for each process
* <code>river_desc.nc</code>: output with river description (optional, only when routing is activated)

== Running the model in DCAO's computational lab ==
Follow this link [[runORDCAO]] to set-up the runs in the machines of DCAO's computational laboratory

= OR4L: L. Fita's work-flow management for ORCHIDEE =
ORCHIDEE should be run with [http://forge.ipsl.jussieu.fr/libigcm libIGCM] which is a work-flow management for ORCHIDEE developed at the IPSL.

However, L. Fita developed an independent simpler and less potent work-flow called OR4L. See how it works in this wiki page [[ORCHIDEE/OR4L OR4L]]

= OR_1proc: DCAO's 1-proc work-flow management for ORCHIDEE =
DCAO's computational lab machines are 1 processors standard machines. A new work-flow management has been created for such cases. Mostly related to the UMI & DCAO course of [[http://www.cima.fcen.uba.ar/UMI/wrk/modelado-2019.php land-atmosphere interaction and its modelling]]. All the iformation is available in the wiki page [[OR1proc OR 1proc]]

ORcompHYDRA hydra

2023-01-23T18:46:55Z

Lucia.cappelletti: /* Installation steps using modipsl */

Compilation at CIMA's HPC 'hydra'

= Installation steps using modipsl =
Go to the installation directory <code>[INSTALLDIR]</code> (for hydra <code>[INSTALLDIR]=/share/ORCHIDEE</code>)
<pre>$ cd [INSTALLDIR]</pre>

Instalation requirements: <code>svn, ksh. </code>

Getting the IPSL-models suite (trunk), following this [https://forge.ipsl.jussieu.fr/orchidee/wiki/DevelopmentActivities/ORCHIDEE-CNP/howtoUse link]
<pre>$ svn co --username icmc_users https://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl</pre>


Going to the <code>util</code> folder:
<pre>$ cd modipsl/util</pre>

Getting the off-line version of ORCHIDEE (see components in file <code>mod.def</code>)
<pre>$ ./model ORCHIDEE_trunk >& run_get_model.log</pre>

We got some issues with the ports, thus, it needs to be manually done:
<pre>$ cd ../modeles</pre>

Getting IOIPSL:
<pre>$ mkdir -p IOIPSL/src
$ svn co https://forge.ipsl.jussieu.fr/igcmg/svn/IOIPSL/tags/v2_2_2/src IOIPSL/src</pre>

Getting XIOS library
<pre>
$ svn co -r 1043 https://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk XIOS
</pre>

Getting ORCHIDEE:
<pre>
$ svn co svn://forge.ipsl.jussieu.fr/orchidee/trunk ORCHIDEE
</pre>

By the end one should have:
<pre>$ ls
IOIPSL ORCHIDEE XIOS</pre>

Going back to <code>util</code> to proceed
<pre>$ cd ../util</pre>


These are the final versions of the codes
* ORCHIDEE: 4622
* ORCHIDEE_OL: 4622
* IOIPSL: 3379
* XIOS: 1043

Preparing compilation environment for <code>hydra</code>. One need to add into <code>AA_make.gdef</code> specifications for <code>hydra</code> (at the end of file):
<pre>
#-Q- ifort_hydra #- Global definitions for hydra, ifort
#-Q- ifort_hydra LIB_MPI = MPI1
#-Q- ifort_hydra LIB_MPI_BIS = MPI1
#-Q- ifort_hydra FCM_ARCH = ifort_hydra
#-Q- ifort_hydra M_K = make
#-Q- ifort_hydra P_C = cpp
#-Q- ifort_hydra P_O = -P -C -traditional $(P_P)
#-Q- ifort_hydra F_C = /usr/local/bin/mpif90 -c -cpp
#-Q- ifort_hydra #-D- MD F_D = -g
#-Q- ifort_hydra #-D- MN F_D =
#-Q- ifort_hydra #-P- I4R4 F_P = -i4
#-Q- ifort_hydra #-P- I4R8 F_P = -i4 -r8
#-Q- ifort_hydra #-P- I8R8 F_P = -i8 -r8
#-Q- ifort_hydra F_O = -DCPP_PARA -O3 $(F_D) $(F_P) -I$(MODDIR) -module $(MODDIR) -fp-model precise
#-Q- ifort_hydra F_L = /usr/local/bin/mpif90
#-Q- ifort_hydra M_M = 0
#-Q- ifort_hydra L_X = 0
#-Q- ifort_hydra L_O =
#-Q- ifort_hydra A_C = ar -rs
#-Q- ifort_hydra A_G = ar -x
#-Q- ifort_hydra C_C = cc -c
#-Q- ifort_hydra C_O =
#-Q- ifort_hydra C_L = cc
#-Q- ifort_hydra #-
#-Q- ifort_hydra NCDF_INC = /usr/local/include
#-Q- ifort_hydra NCDF_LIB = -L/usr/local/lib -lnetcdf -lnetcdff
#-Q- ifort_hydra #-
</pre>
* Creation of the configuration <code>arch</code> files for the compilation of each component

== XIOS ==
** going there:
<pre>$ cd ../modeles/XIOS/arch</pre>
** Using CICLAD's ifort compilation as reference
<pre>$ cp arch-ifort_CICLAD.fcm arch-ifort_hydra.fcm</pre>
** Adapting values (following ifort bug issue for version 12.0.3, [https://software.intel.com/en-us/forums/intel-c-compiler/topic/289446 ifort bug]):
<pre>%CCOMPILER /usr/local/bin/mpicc
%FCOMPILER /usr/local/bin/mpif90
%LINKER /usr/local/bin/mpif90 -nofor-main

%BASE_CFLAGS -std=c++0x
%PROD_CFLAGS -O3 -D BOOST_DISABLE_ASSERTS
%DEV_CFLAGS -g -traceback
%DEBUG_CFLAGS -DBZ_DEBUG -g -traceback -fno-inline

%BASE_FFLAGS -D__NONE__
%PROD_FFLAGS -O3
%DEV_FFLAGS -g -O2 -traceback
%DEBUG_FFLAGS -g -traceback

%BASE_INC -D__NONE__
%BASE_LD -lstdc++

%CPP /usr/local/bin/mpicc -EP
%FPP cpp -P
%MAKE gmake</pre>
** Getting paths:
<pre>$ cp arch-ifort_CICLAD.path arch-ifort_hydra.path</pre>
** Adapting values:
<pre>NETCDF_INCDIR="-I/usr/local/include"
NETCDF_LIBDIR="-L/usr/local/lib"
NETCDF_LIB="-lnetcdf -lnetcdff"
MPI_INCDIR=""
MPI_LIBDIR=""
MPI_LIB=""
HDF5_INCDIR=""
HDF5_LIBDIR=""
HDF5_LIB=""</pre>

== ORCHIDEE ==
** Going there
<pre>$ cd ../../ORCHIDEE/arch</pre>
** Using CICLAD's ifort compilation as reference
<pre>$ cp arch-ifort_CICLAD.fcm arch-ifort_hydra.fcm</pre>
** Adapting values:
<pre>%COMPILER /usr/local/bin/mpif90
%LINK /usr/local/bin/mpif90
%AR ar
%MAKE gmake
%FPP_FLAGS -P -traditional
%FPP_DEF
%BASE_FFLAGS -i4 -r8 -fp-model precise
%PROD_FFLAGS -O3
%DEV_FFLAGS -g -O2 -traceback -fp-stack-check -ftrapuv -check bounds
%DEBUG_FFLAGS -fpe0 -O0 -g -traceback -fp-stack-check -ftrapuv -check bounds -check all
%MPI_FFLAGS
%OMP_FFLAGS -openmp -openmp-threadprivate compat
%BASE_LD -i4 -r8
%MPI_LD
%OMP_LD -openmp</pre>
** getting paths
<pre>$ cp arch-ifort_CICLAD.path arch-ifort_hydra.path</pre>
** Adapting values:
<pre>NETCDF_LIBDIR="/usr/local/lib -lnetcdf -lnetcdff -lstdc++"
NETCDF_INCDIR=/usr/local/include
IOIPSL_INCDIR=../../../lib
IOIPSL_LIBDIR=../../../lib
XIOS_INCDIR=${ORCHDIR}/../XIOS/inc
XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"</pre>

== Bulding & compiling ==
** Going back to <code>util</code> to proceed
<pre>$ cd ../../../util</pre>
** Installing the code:
<pre>$ ./ins_make -t ifort_hydra >& run_ins_make.log</pre>
** Going there:
<pre>$ cd ../config/ORCHIDEE_OL</pre>
** No need to loading the right environment since in <code>hydra</code> its by default
** Compiling XIOS in sequential (in <code>Makefile</Code>, adding no-parallel compilation):
<pre>./make_xios --netcdf_lib netcdf4_seq (...)</pre>
** Compiling:
<pre>$ gmake >& run_gmake.log</pre>
** Checking if everything went fine:
<pre>$ cat -n run_gmake.log | grep Error
$ cat -n run_gmake.log | grep undefined
$ ls ../../bin/
orchidee_ol xios_server.exe</pre>

= Compiling rebuild =

Due to the fact that <code>hydra</code> does not have the netcdf libraries compiled in parallel, ORCHDEE output is written with multiple files being a file for each process. In order to overcome this output. IPSL does prepare a tool to join the files and provide the expected output. This tool is called <code>rebuild</code> (a Kornshell script which encapsulates de exacutable <code>flio_rbld</code>) and it comes with the <code>IOIPSL</code> libraries. The IOIPSL libraries, are a set of old libraries developed by the IPSL (M. A. Foujuls, J. Polcher among others) to deal with the netCDF data access for all the models developed at the IOIPSL. Compiling IOIPSL (following [http://lmdz.lmd.jussieu.fr/utilisateurs/faq-en/installation/comment-installer-ioipsl-et-loutil-rebuild install rebuild]. It has to be compiled independently. Here it is explained how it has to be done.

* Go to the instalation directory <code>[INSTALLDIR]</code> (at hydra <code>share</code>)
<pre>$ cd [INSTALLDIR]</pre>
* getting the last version of the code
<pre>$ svn co https://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl_IOIPSLtools</pre>
* going to prepare compilation/installation
<pre>$ cd modipsl_IOIPSLtools/util</pre>
* preparing environment
<pre>./model IOIPSL_PLUS</pre>
* We got some issues with the ports, thus, it needs to be manually done:
<pre>$ cd ../modeles</pre>
* Getting IOIPSL ('''NOTE:''' notice the difference in library's version from the previous one):
<pre>$ svn co https://forge.ipsl.jussieu.fr/igcmg/svn/IOIPSL/tags/v2_2_3 IOIPSL</pre>
* Comming back to the <code>util</code> folder
<pre>$ cd ../util</pre>
* Creation of the compilation environment for <code>`hydra'</code> using <code>'ifort'</code> inside <code>AA_make.gdef</code> as in the full compilation
<pre>$ cp ../../modipsl/util/AA_make.gdef ./</pre>
* Preparing makefiles
<pre>$ ./ins_make -t "ifort_hydra" -p I4R8</pre>
* going to src folder to compile
<pre>$ cd ../modeles/IOIPSL/src</pre>
* cleaning (you never know...)
<pre>$ make clean</pre>
* compiling
<pre>$ make >& run_make.log</pre>
* Checking no errors:
<pre>$ cat -n run_make.log | grep Error</pre>
* compilation of tools (file concatenation)
<pre>$ cd ../tools </pre>
* cleaning (you never know...)
<pre>$ make clean</pre>
* compiling
<pre>$ make >& run_make.log</pre>
* Checking no errors:
<pre>$ cat -n run_make.log | grep Error</pre>
* One should have:
<pre>$ ls ../../../bin/
flio_rbld rebuild</pre>

= debug Instalation =
Getting a debugging copy for test purposes

== Instalation steps using modipsl ==
* Go to the instalation directory <code>[INSTALLDIR]</code> (<code>/share</code> in <code>hydra</code>)
<pre>$ cd [INSTALLDIR]</pre>
* Getting the IPSL-models suite (r 3379)
<pre>$ svn co https://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl_dbg</pre>
* Once we got the codes, we need to copy the specificities of the installation for <code>hydra</code>
<pre>$ cp ../../modipsl/util/AA_make.gdef ./
$ cp ../../modipsl/modeles/XIOS/arch/*hydra* ../modeles/XIOS/arch/
$ cp ../../modipsl/modeles/ORCHIDEE/arch/*hydra* ../modeles/ORCHIDEE/arch/</pre>
* Everything is the same as for the installation, except that we need to indicate debugging compilation:
<pre>./ins_make -t ifort_hydra -d >& run_ins_make.log</pre>
* And on <code>Makefile</code> from <code>config/ORCHIDEE_OL</code>, change all the <code>-prod</code> by <code>-debug</code>
<pre>(...)
xios :
(cd ../../modeles/XIOS ; ./make_xios --netcdf_lib netcdf4_seq \
--debug --arch ${FCM_ARCH} --job 8 ; cp bin/xios_server.exe ../../bin/. ; )
(...)
driver :
(cd ../../modeles/ORCHIDEE ; ./makeorchidee_fcm -j 8 -parallel mpi -debug -arch ${FCM_ARCH} -driver ; )
(...)
driver_xios :
(cd ../../modeles/ORCHIDEE ; ./makeorchidee_fcm -xios2 -j 8 -parallel mpi -debug -arch ${FCM_ARCH} -driver ; )
(...)</pre>
* Compiling:
<pre>$ gmake >& run_gmake.log</pre>
* Checking if everything went fine:
<pre>$ cat -n run_gmake.log | grep Error
$ cat -n run_gmake.log | grep undefined
$ ls ../../bin/
orchidee_ol xios_server.exe</pre>

ORCHIDEE

2023-01-23T14:21:27Z