Notes on Downloading/Running NEMO 3.4 on Ocean Cluster including Salish

Note, this set-up runs on one core on one processor.

Getting the Code

• Goto https://www.nemo-ocean.eu/

• Logon.

• Goto Using NEMO, then User Guides, the NEMO Quick Start Guide

• locally switch to BASH as your shell (e.g. type bash)

• check perl is installed (type perl and cntrl C when it sits on the new line wang)

• check svn is installed (type svn, it will suggest help for you)

• check you have a fortran compiler (on our systems gfortran)

• netcdf (not sure yet how you check this)

• then type

  svn --username "sallen@eos.ubc.ca" co -r 3819 http://forge.ipsl.jussieu.fr/nemo/svn/branches/2012/dev_v3_4_STABLE_2012
  

• EXCEPT change my username to your username on the NEMO system.

• NOTE no < before svn unlike what they have on the website

• You will be prompted for your password

• and now you have the code

Making a Project

• Nemo uses an ARCH (architecture) file to determine compiler, maker, netcdf library location.

  cd dev_v3_4_STABLE_2012/NEMOGCM/ARCH
  

• NEMO ships with a gfortran_linux file. This file needs some edits to work on ocean. Changes in bold.

• New ARCH file: arch-ocean.fcm containing:

  # generic gfortran compiler options for linux
  # NCDF_INC    netcdf include file
  # NCDF_LIB    netcdf library
  # FC          Fortran compiler command
  # FCFLAGS     Fortran compiler flags
  # FFLAGS      Fortran 77 compiler flags
  # LD          linker
  # LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a
  # FPPFLAGS    pre-processing flags
  # AR          assembler
  # ARFLAGS     assembler flags
  # MK          make
  # USER_INC    additional include files for the compiler,  e.g. -I<include dir>
  # USER_LIB    additional libraries to pass to the linker, e.g. -l<library>
  %NCDF_INC            **-I/usr/include**
  %NCDF_LIB            **-L/usr/lib -lnetcdff**
  %FC                  gfortran
  %FCFLAGS             -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer
  %FFLAGS              %FCFLAGS
  %LD                  gfortran
  %LDFLAGS
  %FPPFLAGS            -P -C -traditional
  %AR                  ar
  %ARFLAGS             -rs
  %MK                  **make**
  %USER_INC            %NCDF_INC
  %USER_LIB            %NCDF_LIB
  

• then change directory and make a project, e.g. then for a new GYRE configuration using your new arch file ocean

• Note we need to add the key_nosignedzero for our fortran 90 compiler

• Add the netcdf4 key to use netcdf4 capabilities

  cd ../CONFIG
  ./makenemo -m ocean -r GYRE -n MY_GYRE add_key "key_nosignedzero key_netcdf4"
  

  • If you are compiling version 3.6 on salish use the following command instead:

     cd ../CONFIG
    ./makenemo -m GCC_SALISH -r GYRE -n MY_GYRE -j8
    

• If the following error comes up:

  /* Copyright (C) 1991-2012 Free Software Foundation, Inc.
   1
  Error: Invalid character in name at (1)
  

  then modify the arch-ocean.fcm file line:

  %FPPFLAGS        -P -C -traditional
  

  to:

  %FPPFLAGS        -P -traditional
  

Running the Code

cd MY_GYRE/EXP00
nice ./opa