NetCDF library at Obelix, LSCE cluster

21 January 2015

The version of the netcdf library used in ORCHIDEE has been changed for use at obelix, the LSCE cluster. netcdf has changed from netcdf-3.6.2 into netcdf-4.3.2p. The library hdf5 has also been added at the same time as it is needed for linking with XIOS.

There are 3 changes related in following components:

• the trunk of ORCHIDEE, since see changeset révison [2481] at ORCHIDEE trunk repository
• trunk of LMDZ5, since changeset ​2184 at LMDZ5 SVN repository
• trunk of modipsl, since changeset ​revision 2398 at modipsl SVN repository

changes related to the netcdf library used for ORCHIDEE and LMDZ at obelix (cluster at LSCE). If you reinstall the latest version of the trunk of ORCHIDEE and/or LMDZ together with the latest version of modipsl, these changes will be taken into account without you having to change anything. Please read below to have more information about what has been done. Old executables should continue working without any problem. No change in results has been seen related to these changes.

Compiling

Same version of netcdf must be used in all components forming one executable. netcdf is specified among the compiling options at 3 places and must be the same at these 3 places (only 2 for ORCHIDEE offline):

• modipsl for IOIPSL (in the file modipsl/util/AA_make.gdef)
• the source code for ORCHIDEE (in ORCHIDEE/arch/arch-ifort_LSCE.path)
• the source code for LMDZ (in LMDZ/arch/arch-ifort_LSCE.path)

Important using other versions than the trunk ORCHIDEE:

• If you reinstall a new modipsl, you'll have the latest version using netcdf-4.3.2p for IOIPSL. If the other components that you install are older or coming from a branch or personal version, you must update the file arch-ifort_LSCE.path as done here [2481].

• Branches and personal versions of ORCHIDEE needs to be updated and commited.

Running

To run the new executable containing the dynamic library netcdf4p, a "module load netcdf/4p" is needed during run time. This is done automatically if you run with libIGCM. For this the file /home/users/igcmg/.atlas_env_asterix_ksh which is sourced by libIGCM is changed. Old executable with netcdf-3.6 can still be used with the same job. If you run without libIGCM, following must be put in your job :

. /usr/share/Modules/init/ksh
module load netcdf/4p

where the first line is only to be added for ksh jobs to access the command module.

Possible errors

• You install a new modipsl with another version of ORCHIDEE than the trunk, see compiling above
• You update your ORCHIDEE trunk version in an old version of modipsl : ORCHIDEE will contain netcdf4p but modipsl 3.6.2. Reinstall everything or update modipsl with

  cd modipsl/util
  svn update