WhatIs: The install lmdz.sh script

The install_lmdz.sh script is a Bash script that aims at being an "installer" for LMDZ of Linux machines.

In practice it runs a succession of mandatory steps to install and run the model from scratch, namely:

• Download and install required libraries (NetCDF, IOIPSL and possibly XIOS)
• Download the source code (LMDZ and ORCHIDEE), compile it and run a test (bench) simulation

It has many options and features; a good starting point (short of reading and digesting the Bash script itself) is to run install_lmdz.sh -h to learn about these, which should yield something like:

install_lmdz.sh
    ./install_lmdz.sh [ -v version ] [ -r svn_release ]
           [ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
           [-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]

    -v       "version" like 20150828.trunk
             see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk

    -r       "svn_release" : either the svn release number or "last"
    
    -compiler gfortran|ifort|pgf90 (default: gfortran)

    -parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)

    -d        GRID_RESOLUTION should be among the available benchs if -bench 1
              among which : 48x36x19, 48x36x39
              if wanting to run a bench simulation in addition to compilation
              default : 48x36x19

    -bench     activating the bench or not (0/1). Default 1

    -name      LOCAL_MODEL_NAME : default = LMDZversion.release

    -netcdf    PATH : full path to an existing installed NetCDF library
               (without -netcdf: also download and install the NetCDF library)  
    
    -xios      also download and compile the XIOS library
               (requires the NetCDF4-HDF5 library, also installed by default)
               (requires to also have -parallel mpi_omp)

    -gprof     to compile with -pg to enable profiling with gprof

    -cosp      to run without our with cospv1 or cospv2 [none/v1/v2]
 
    -rad RADIATIF can be old, rrtm or ecrad radiatif code

    -nofcm     to compile without fcm

    -SCM        install 1D version automatically

    -debug      compile everything in debug mode

    -opt_makelmdz     to call makelmdz or makelmdz_fcm with additional options

    -physiq    to choose which physics package to use

    -env_file  specify an arch.env file to overwrite the existing one

    -veget surface model to run [NONE/CMIP6/xxxx]

Note that the install_lmdz.sh script is not the only way to install LMDZ; one can manually do the various key steps (quite possibly adapted to the specificities of the machine that is used).

02/12/2021

---

New install_lmdz version (Amaury - 06/2024)

Known bugs / issues

ORCHIDEE bench

Right now (06/24), only the CMIP6/orch2.0 ORCHIDEE version has a proper bench. As a result, other versions (orch2.2, orch4/trunk) run in a bench that doesn't activate ORCHIDEE.

Todo: make a proper orch2.2 and orch4 bench, with/without xios)

Debug mode crashes

When activating -debug, with newer versions of NETCDF, a segfault is raised on lines such as CALL err(NF90_OPEN(var,NF90_NOWRITE,fID),"open",var). It seems that the segfault originates from the NF90_OPEN function itself.

Todo: check with even newer versions of netcdf - but then we face the other documented netcdf bug...

ORCHIDEE 4/TRUNK compilation fails

ORCHIDEE 4/trunk can't be compiled with gfortran for now. This issue has been raised to the ORCHIDEE team (06/24).

Todo: update when orch fixes their code

Error -105 in closing file

with -parallel mpi_omp -veget orch2.0, at the end of a simulation, we can read in listing:

WARNING FROM ROUTINE restclo
--> Error   -105 in closing file : ***
--> sechiba_rest_out.nc
--> 

This "error" doesn't seem to actually affect the outputs, and should be ignored; yet, its cause hasn't been investigated.

Compilation with newer netcdf/hdf5

install_lmdz can't be used with very recent netcdf/hdf5 libraries.

TODO: add specific versions, + error messages