Frequently Asked Questions


Script problem
Problem of configuration where mychimere.sh.example is removed
I want to configure my mychimere.sh file but it is deleted when trying to configure the model
Solution:
  • You have to specify a name that is NOT mychimere.sh.example, otherwise it just erases this template file.
  • The typical command line is:
    ./config.sh mychimere.sh.myconfig 
    
  • You can download again the mychimere.sh.example here.


Compilation problem
The compilation failed with the following error message:
Fatal Error: While reading module 'netcdf' found module version 0, expected 8.
Solution:
  • The netcdf library specified in the current Makefile.hdr has been compiled with a different compiler version than the one used for CHIMERE compilation
  • Recompile the netcdf library with the same compiler version as that used to compile CHIMERE


Compilation problem
Strange compiler error messages that refer to a compiler other than the one used to compile CHIMERE, e.g.
gfortran: unrecognized option '-cpp'
when compiling CHIMERE with g95.
Solution:
  • Your MPI library was built with a compiler different from the one used to compile CHIMERE (in the case above Open MPI was built with gfortran).
  • Recompile your MPI library or use another compiler with CHIMERE, so that the same compiler is used.


Compilation question
Is it necessary to recompile the CHIMERE code before each run?
Solution:
  • Until version 2014b, it was necessary to recompile when changing the domain or the subdomains number (nzdoms, nmdoms).
  • But now, you only need to recompile if you change something in the Fortran code. Otherwise, just put imakecompil to 0 in your chimere.par.


Compilation question
When the libraries used, there is a problem reading the soil and surface databases. The error message is:
domains-extract_geog.F90: netCDF error on source line         118 NetCDF: Unknown file format
 Error code is          -51
STOP 1 
Solution: It is the kind of error you have when you try to open a netcdf4 file with a netcdf3.x library version. For the CHIMERE development, we are running the model with netcdf-4.3.1.1 and hdf5-1.8.12, and it works. But we tested only this configuration and we can not guarantee that all libraries are working well with the model.

Simulation question
Is it possible to vertically extend CHIMERE beyond 500 mb (~5km)?
Solution:
  • Yes. Starting from chimere2014 version, the FastJ radiative transfer model is included in CHIMERE to compute photolysis reaction rates. This makes it possible to extend the model domain vertically beyond 500 hPa.
  • But: Note that above 200hPa (~10km amd UTLS), the chemistry is not realistic
bugs and updates

  • This page lists the bugs found in the current last CHIMERE version and the updates to add in order to have a more secure code.
  • Each time a bug is found, the corresponding chimere version has a new name: the letter at the end of the name version is increased by a letter (from "A" to "B" for example).
  • If a slight update is necessary, the file is displayed on this page only


Model version Description Reported or Found by... Download or correct
chimere2017r4 pnetcdf 1.9.0, among other changes (https://trac.mcs.anl.gov/projects/parallel-netcdf/wiki/ReleaseNotes-1.9.0) has raised the value of NF_MAX_VAR_DIMS from 1024 to 2147483647. Unfortunately, the pncvar input/output module of CHIMERE uses this parameter to allocate memory to some arrays, and this huge value would just freeze the model and/or make it crash due to insufficient memory.
Save and recompile the model.
This bugfix applies to all the recent versions of CHIMERE (versions that have a src/pncvar.F90 routine). Even though the patch is technically necessary only if you wish to use pnetcdf 1.9.0 or above, the patched version will work with earlier pnetcdf versions as well, so I would advise users to make the change anyway to avoid bad surprises and inexplicable crashes when the pnetcdf library gets upgraded on your system.
S.Mailler (May 2019) The bugfix for this is easy :
  • Edit manually the src/pncvar.F90 routine
  • Replace all occurences of NF_MAX_VAR_DIMS by 32 throughout the file
chimere2017r4 Problem with the anthropogenic emissions when using the point sources. Replace the following Fortran routine and recompile M.Stortini (January 2019) prep_aemis.F90
chimere2017r4 Problem with chemprep when mineral dust option 'iusedust' is set to zero
You may have this error message when preparing the chemistry and if you selected iusedust=0.
Building output species list
cp: cannot stat 'input-fastj_1.txt': No such file or directory
rm: cannot remove 'input-fastj_1.txt': No such file or directory
Abnormal termination of prep-chemistry-data.sh
Replace the following script (after removing _bugfix in the filename)
L.Menut (September 2018) chemprep-prep-chemistry-data.sh_bugfix
chimere2017r4 Force the use of an interpolation for the surface pressure (in case of WRF use, not always stable). Replace the two following subroutines (after removing _bugfix in the filename) L.Menut (July 2018) calc_turb.F90_bugfix
calc_deepconv.F90_bugfix
chimere2017r4 Corrects a problem in the creation of boundary conditions of nested domains A.Royer (October, 2017) chimere-step1.sh
emiSURF2016b Correction of the EMEP grid coordinates M.Valari (October, 2017) COORD_EMEP50x50
chimere2017 Bug fixes in atmphys.F90 and worker_message_subs.F90: WRF surface pressure for the case of CHIMERE grid identical to that of WRF; size of MPI mesages A.Deroubaix, D.Khvorostyanov (March, 2017) atmphys.F90; worker_message_subs.F90
chimere2017 Bug fix in domains-extract_geog.F90 for the vegetation fraction S.Mailler, L.Menut (March, 2017) domains-extract_geog.F90
chimere2013b Fixed bug in prep_chimere.F90 for the case where the coarse simulation output is in ug/m3 Adrien Royer/Sandy Adriaenssens
(March, 2014)
prep_chimere.F90


scripts


WARNING:
The following scripts are developed by the CHIMERE developer team for internal use.
They are offered as examples but are not maintained and there is no user support (contrarily to the CHIMERE model).


Description Date Authors
Perform a chained simulation
The command line for a simulation enables to give a strting date a simulation duration (in days). If you want to produce a long simulation, but several "out" output files with a length of a few days, you can use the 'restart' capability of the model. For example, you can use this script:
#!/bin/sh
export LANG=en_US
export LC_NUMERIC=C
export LC_ALL=C

firstdate=20130115
lastdate=20131230
parfile=chimere.par.anMED
nh=120
incday=5

di=${firstdate}

./chimere.sh ${di} ${nh} c ${parfile} || exit 1
   
while [ $di -le $lastdate ] ; do
   ./chimere.sh ${di} ${nh} f ${parfile} || exit 1
   di=`date -u -d "$di $incday days" +%Y%m%d`
done
2018 L.Menut
Reformat TNO anthropogenic emissions inventory to be read by the CHIMERE EMISURF program 2017 Michael Russo,
University of Aveiro, GEMAC, CESAM
michaelarusso@ua.pt
Download EMEP emissions on the 50 km grid (starting from the emiSURF2016 version)
  • Download the script dl_emep.sh
  • Run the script, e.g. ./dl_emep.sh 2012. This creates file emep_2012.txt
  • Put the *.txt file to the annual-EMEP50x50/50x50new/data_expert directory of your emiSURF installation.
2017 G.Siour
Generate CHIMERE domain file COORD_xxx from a WRF meteorological output file
  • Download the script wrfcoord.py
  • Make sure you have a python installation with netCDF4 and numpy libraries. If not, you can use pip or easy_install or Anaconda, etc. to install them.
  • Run the script.
  • Rename the generated .CHI file to COORD_Your_Domain_Name
  • Put it to the chimere_root/domains/HCOORD directory.
2012 D.Khvorostyanov