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
Sommaire
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
COSP + orch + xios segfault
With -veget orch2.0 -xios -cosp v1 (or v2), we encounter a segfault in the bench.
Unfortunately because of the netcdf debug bug (see above), we can't get to the actual trace....
