Beginner (#3) - [FAQ] Getting started with NEMO, please read this before creating a new topic (#8) - Message List

[FAQ] Getting started with NEMO, please read this before creating a new topic

FAQ: Getting started with NEMO

Last edition: 2018-06-22 07:43 CEST by

Please check the information in this page before creating a new item in this forum. The list of questions and answer is available in the page outline on the right side of this page

Suggested first steps

As beginner with NEMO, or when you change computing platform, it is strongly recommended you first download the up-to-date release of NEMO and run at least one of the Reference Configurations available with the release: those reference configurations are indeed working fine with the release so that this first step allows the user to check everything is working properly once installed locally.

Downloading NEMO

A detailed guide to download/install the source code is available in the model install section

I cannot download NEMO using subversion

Trying to download NEMO using svn co (checkout), I get no answer or an error message like

svn: OPTIONS of '': could not connect to server

This may be related to the subversion proxy setting. Indeed, some organizations will limit external communications (such as SVN traffic) through specified external-facing machines and ports for security reasons. If so, you will need to tell subversion where this machine is and how to access it (i.e. the port number it has assigned for the external communication you wish to perform):
In your home directory there should be a directory called .subversion. In this directory there is a file named 'servers' which controls a number of subversion features. It's usually a rather long text file with most of lines commented out. Search for ' [global] '. Under this stanza heading, there should be two lines as so:

http-proxy-host = <name_of_some_proxy_machine>
http-proxy-port = <number>

There will some default values for the name of the proxy machine and port number. Replace these default values with those used at your local site. You will have to get the name of proxy machine and port number from your local system administrator or IT department.

Building the executable

Detailed guide to download/install the source code is available in the model install section

Error message when launching makenemo

If you get a long error message at the beginning of the process pointing errors in some FCM (*.pl files), it is probably that the version of perl installed on your computer is not the right one. Make sure you are using at least Perl 5.10 (or newer).

Where are the outputs of the compiler

Compiler outputs such as executable file, pre-processed fortran files, object files etc. are located in the NEMOGCM/CONFIG/[CONFIG_NAME]/BLD sub-folders. If activating the compiler option to get compiler output listing ( -list option for ifort compiler), the output listings are in BLD/tmp.

Using a new computer

Compiler and linker options on a platform are defined through the arch file you select in the -m option of the makenemo command.
All arch files available are in NEMOGCM/ARCH directory. Choose an existing file or build a new one starting from the closest existing one. See more details in model install page section3.

Running your application

Where are the execution outputs

Where are execution error messages

All the printed outputs and error messages are located in the ocean.output file. This file is quite big, and more information is needed to located precisely the errors.
During execution, the whole initialisation phase is scanned before NEMO stops on one or more errors. This allows to get informations on all errors at once. To find details on each error, search for E R R O R and W A R N I N G (in capitals and with a space between each letter) in the ocean.output file to find occurrence of errors, warning and explanations.

When running with MPI, if an error occurs on a rank (processor, cpu, core) that is not the one writing the log file, then it might happen that the reason for the error is not communicated to the log writing rank. You can set

 ln_ctl = .true.

in the namelist_cfg of your experiment to generate an ocean.output file per rank.

NEMO crashed with XIOS error on axis.cpp

Error [CAxis::checkAttributes(void)] : In file '../xios-1.0/src/node/axis.cpp',
line 88 -> The bounds array of the axis [ id = 'deptht' , context = 'nemo' ] must be of dimension axis 2 x size
Axis size is 31
Bounds size is 31 x 2

The 3.6 release of NEMO is compatible with XIOS 1.0 branch up to r703, from there the source code has to be edited (not recommended for NEMO beginners).
More information on XIOS configuration page.


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