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 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)
svn --username "firstname.lastname@example.org" 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.
NEMO ships with a gfortran_linux file. This file needs some edits to work on ocean. Changes in bold.
New ARCH file:
# 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
salishuse 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
%FPPFLAGS -P -traditional
Running the Code¶
cd MY_GYRE/EXP00 nice ./opa