wiki:Doc/Config/LMDZOR_v6.1

Version 15 (modified by pinsard, 8 years ago) (diff)

typo

The LMDZOR_v6 configuration

Table of contents

  1. 1. Description
    1. 1.1. Main differences with LMDZOR_v5 and LMDZOR_v5.2
    2. 1.2. Compiling
    3. 1.3. Launching
    4. 1.4. XIOS and output control
    5. 1.5. Parameter files
    6. 1.6. COSP and NMC output
  2. 2. Quick installation
  3. 3. Simulations

Table of contents

  1. 1. Description
  2. 2. Quick installation
  3. 3. Simulations

LMDZOR_v6 is a configuration under construction. It can already be used but it is not in its final version. More information to come...

Person in charge: Josefine Ghattas

1. Description

LMDZOR_v6 configuration contains the atmospheric model LMDZ and the land surface model ORCHIDEE. Currently this configuration contains the following components:

  • LMDZ5 testing revision 2314
  • ORCHIDEE trunk revision 2724
  • XIOS branchs/xios-1.0 revision 604 (library for writing output files)
  • IOIPSL (IOIPSL is not used for output anymore, only for restart files and other options)
  • libIGCM trunk revision 1215
  • configuration files for LMDZOR_v6 revision 2618

Default compilation is still 96x96x39. Default option during run time is old physics and 2-layer hydrology. These options can be changed.

1.1. Main differences with LMDZOR_v5 and LMDZOR_v5.2

LMDZOR_v6 :

  • is adapted to the latest versions of LMDZ and ORCHIDEE.
  • is only using XIOS for writing diagnostics. All diagnostics are configured in the xml files read by XIOS. The use of XIOS in server mode(default set up) removes the need for rebuild.
  • is compiling the hybrid parallelism mode (mixed MPI-OPenMP) which means that more cores can be used during run time which speeds up the computing time.
  • has a clearer method for changing parameter files : the drivers can only change parameters set equal AUTO in the parameter files
    • variables marked as _AUTO_ in the parameter files can be changed by the users. They can not be changed again by the scripts (the drivers). For example this is the case for all variables concerning the output. The user can set the output level as she wants directly into the PARAM/file_def_...xml files and it can not be overwritten by the drivers.
    • variables marked as _AUTOBLOCKER_ must not be changed. If still they are changed, the simulation will stop with error message because the drivers are not allowed to make hidden modifications.

1.2. Compiling

Default compilation is still 96x96x39 but other resolutions can be compiled. To compile 144x142x79 grid do as follow : 

gmake LMD144142-L79

By default the compiling is done for hybrid MPI and OMP parallelism. It is not necessary to activate OMP threads during run time.

1.3. Launching

The default set up is using 31MPI for the gcm.e and 1MPI for the xios server. This is set in config.card : 

#-- Total Number of Processors
JobNumProcTot=32
...
[Executable]
ATM= (gcm.e, lmdz.x, 31MPI, 1OMP)
SRF= ("", "")
SBG= ("", "")
IOS= (xios_server.exe, xios.x, 1MPI)

See here an example using more MPI and 2 threads OMP (case suitable for 144x142x79), note that the heading for the job must be adapted as well: 

JobNumProcTot=95
...
#========================================================================
#D-- Executable -
[Executable]
ATM= (gcm.e, lmdz.x, 47MPI, 2OMP)
SRF= ("", "")
SBG= ("", "")
IOS= (xios_server.exe, xios.x, 1MPI)

1.4. XIOS and output control

XIOS is the new component used for output writing. It consists of a library linked to the model and an external server executable (xios_server.exe). It can be launched in attached mode or in server mode. The default set up in LMDZOR_v6 is using the server mode with 1 MPI for the server. 2 executables are launched: gcm.e and xios_server.exe. No reconstruction is needed for the output files. The rebuild tool detects automatically that this is not needed.

LMDZOR_v6 is only using XIOS for writing diagnostic output files. The output is managed by xml files. The files beginning with file_def....xml are controlling the variables and the files that are written.

A basic level of output control is done from config.card with the variables WriteFrequency. For LMDZ it is also possible to change the level of output for the files using the variable OutLevel in lmdz.card. Finer control of the output must be done directly in PARAM/file_def_....xml files. Where it is set _AUTO_, it can be replaced manually for example in PARAM/file_def_histday_lmdz.xml : 

        <file id="histday" name="histday" output_freq="1d" output_level="_AUTO_" enabled="_AUTO_">

can be changed into 

        <file id="histday" name="histday" output_freq="1800s" output_level="1" enabled=".TRUE.">

1.5. Parameter files

Most parameter file are found in PARAM/ directory as for the v5 configurations. But some files are now also copied from the model directories. This is the case for field_def_lmdz.xml and field_def_orchidee.xml. In lmdz.card and orchidee.card you can see where the files are taken from.

In the parameter files, some of the variables will be modified after the job is submitted. This is done by the comp.driver: lmdz.driver, orchidee.driver, stomate.driver and xios.driver. All the variables that might be modified are set equal _AUTO_ or _AUTOBLOCKER_. No variable can be modified without having this key word. The values are set according to the options from lmdz.card, orchidee.card, stomate.card and config.card.

A variable which is set to _AUTO_ can also be changed manually in the corresponding file in the PARAM directory. For this case, the driver can not change it again. Some variables are set equal _AUTOBLOCKER_. They cannot be changed. If still they are changed, the job will exit with error message.

New physics in LMDZ:
Only NPv3.2 is added currently. To run another physics version, you need to add the corresponding file physiq.def_L79_NpvXX coming from Abderrahmane Idelkadi simulations in PARAM and activate it in lmdz.card by setting LMDZ_Physics=NpvXX. The other .def files corresponds to what Abderrahmane has except for pmagic which is =0 in LMDZOR_v6. Don't forget to change the compiling.

CWRR 11-layer hydrology in ORCHIDEE:
Change from Choisnel 2-layer into CWRR 11-layer in orchidee.card by setting DefSuffix=CWRR.

1.6. COSP and NMC output

Default compiling is done without COSP. Options to activate COSP are available in lmdz.card but running with COSP output has not been tested.

NMC monthly output are activated by default.

2. Quick installation

# Installation and compilation
svn co http://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl
cd modipsl/util
./model LMDZOR_v6
cd ../config/LMDZOR_v6
gmake      [or gmake LMD144142-L79]

# Experiment setup
cp EXPERIMENT/LMDZOR/clim/config.card .     # => modify at least JobName=MyJobname, DateBegin, DateEnd in config.card
../../util/ins_job
cd MyJobname

# Modify default setup: change physics in lmdz.card (for other physics than AP or NPv3.2 you also need to add physic.def_NPxxx in PARAM/)
# change hydrology(2- or 11- layer) in orchidee.card
ccc_msub Job_MyJobname / llsubmit Job_MyJobname

3. Simulations