NEMO-3.1 and CONCEPTS-110 Reference Repos

These notes describe the NEMO-3.1 and CONCEPTS-110 reference repositories.

The construction of the NEMO-3.1 repo is described in NEMO-3.1 below. The CONCEPTS-110 repo was constructed from the CODE.tar tarball received on 2-Oct-2013 from J-P Paquin.

Also included here is an analysis of the differences between the NEMO/ directory trees in the 2 repos that was done early in the Salish Sea MEOPAR project in Oct-2013.


The following steps took the NEMO-3.1 repo from initialization to a checkout of that could be built on and used to successfully run the GYRE configuration:

  • An svn checkout of the trunk of the modipsl framework was done from That yielded revision 2163. The repo state was tagged as modipsl-r2163.


    At this point the only directories in the modipsl tree that are populated at doc/ and util/. The bin/, config/, lib/, modeles/, and tmp/ directories are empty and therefore not included in the Mercurial repo.

  • Added J-P Paquin’s build script and util/AA_make.gdef from 2-Oct-2013 CODE.tar tarball. The latter is named AA_make.gdef_BIO.

  • Added definitions for util/model script to util/mod.def to get NEMO-3.1 based on those in that file in the 2-Oct-2013 CODE.tar tarball.

  • Used the modipsl/util/model script to obtain the NEMO-3.1 code and other supporting files. The commands to do so were:

    cd modipsl/util
    ./model NEMO_31

    Added the resulting 1295 files (some of which are in .svn/ directories).

  • Added global makefile definitions for and the BIO HPC cluster to util/AA_make.gdef. The source for the former was Paul Myers’ NEMO-3.1 installation on jasper in /home/pmyers/NEMODRAK_3.1/DRAKKAR/modipsl/util/AA_make.gdef. The latter came from uitl/AA_make.gdef in the 2-Oct-2013 CODE.tar tarball.

Build and Run NEMO-3.1


These instructions are included for completeness. The Salish Sea MEOPAR project does not use pristine NEMO-3.1.

  1. Clone the repository from Bitbucket and update it to the NEMO-3.1 tag state:

    hg clone -u NEMO-3.1 ssh:// NEMO-code-3.1
    cd NEMO-code-3.1
    mkdir modipsl/bin modispl/lib modipsl/tmp
  2. Set up a configuration. We’ll use GYRE as an example and assume that we are building and running on jasper:

    cd modispl/util
    ../modeles/UTIL/fait_config GYRE
  3. Edit ../config/GYRE/scripts/BB_make.ldef to add the appropriate pre-processing prefix for the system you are working on (near the end of the file). For jasper that is:

    #-Q- jasper  prefix = -D


    If you are working on a system other than those that already have global makefile definitions in modipsl/util/AA_make.gdef you will need to add an appropriate block of definitions to that file.

  4. Calculate compilation rules, options, and build dependencies so as to create modipsl/modelels/NEMO/WORK/AA_make (which is symlinked to modipsl/config/GYRE/scripts/BB_make):

    cd ../modeles/NEMO


    fait_AA_make must be run from the modipsl/modeles/NEMO/ directory.

  5. Remove any existing Makefiles and create new ones:

    cd ../../util
    ./ins_make -t jasper
  6. On jasper several modules must be loaded prior to compiling and linking:

    module load compiler/intel/12.1
    module load library/intelmpi/
    module load library/netcdf/4.1.3
    module load library/szip/2.1

    That only needs to be done once per login so you may wish to add those commands to your $HOME/.bashrc file (See .bashrc Snippets).

  7. Compile and link the code:

      cd ../config/GYRE
      make clean
    The results of a successful build are:
    * a :file:`../../bin/opa` executable
    * a :file:`../../lib/libioipsl.a` library
    * a :file:`../../lib/oce/libopa.a` library
  8. Run the model:

    cd EXP00

    On jasper the above command is only appopriate for short test runs. Longer runs should be done using a TORQUE batch job script submitted via the qsub command.

Diffs Analysis

The image below shows the results of an analysis of the file-level differences between the NEMO/ directory trees in the NEMO-3.1 and CONCEPTS-110 repos.

  • Green indicates directories in which all files are identical
  • Red indicates directories in which 1 or more files are different
  • Black shows the number of files in the directories and the difference in the number of files between NEMO-3.1 and CONCEPTS-110 when applicable
  • The OPA_SRC/TDE/ directory in purple is present only in the CONCEPTS-110 directory

The numbers of files in each directory were calculated with commands like:

find OPA_SRC/ZDF/* -prune ! -type d | wc -l

In the directories in which the number of files was the same checks for differences between files was done with commands like:

cd NEMO-3.1/NEMO
for file in $(find OPA_SRC/ZDF/* -prune ! -type d);
  diff $CONCEPTS/$file $file;