...
mkdir -p ~/gem/v_5.1.01/GOAS/UQAMmy_basic_modsversion
cd ~/gem/v_5.1.01/GOAS/UQAMmy_basic_modsversion
Clone and checkout
...
GOAS version
(Old place: git clone https://gitlab.com/eccc/gem/gem.git)
git clone https://github.com/ECCC-ASTD-MRD/gem.git
cd gem
git checkout -b b_ 5.1.0-rc6 5.1.0-rc6 # rc6 latest as of 2021/02/10
Change into the directory 'gem':
cd gem
Create work and 'build' directory
1
Create and change into new branch
git checkout -b my_branch
From here on we will refer to this directory as the "gem" directory.
Create 'work' and 'build' directories
In the 'build' In this directory will be your:
- CMakeFiles
- module files
- object files and excecutables,
- executables
In the 'work' directory will be:
- copy of the excecutables
- model scripts,
- example config files,
- example database,
- and you will execute your simulation from here
Since this directory these directories can get large you must not create it them under your home but under you data space.
mkdir -p /path/to/my/work/directory
export MY_WORK_DIR=/path/to/my/work/directory
After you created the work directory you need to create some symbolic links to this directory:
mkdir -p ${MY_WORK_DIR}/build
mkdir -p /path/to/my/work/directory
export ${MY_WORK_DIR}/work
ln -s ${MY_WORK_DIR}/build
ln -s ${MY_WORK_DIR=/path/to/my/work/directory
mkdir build
cd build }/work
Download database
GOAS comes with it's own database (initial conditions, geophysical & climatological fields, driving data). You only need to download it if you want to run any of the GOAS test configurations. Before downloading it I suggest you create a directory for it outside your home and create a symbolic to this directory, called 'gem_dbase'. For example:
mkdir ${MY_WORK_DIR}/work/gem_dbase
ln -s ${MY_WORK_DIR}/work/gem_dbase
Then you If you want to use it you can download it with:
download-dbase.sh .
Part 2
| Ancre | ||||
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Set compiler version
...
and create Makefiles
Change into the 'gem/build' directory and make sure you did export our work directory - see above:
export MY_WORK_DIR=/path/to/my/work/directory
Also, to make things easier further down, set MY_GEM_DIR to the name of your "gem" directory - see above (replace the '...' in the following command!):
export MY_GEM_DIR=.../gem
Change into the 'gem/build' directory:
cd ${MY_GEM_DIR}/build
Depending on which machine you work and which compiler or environment you want to use the commands differ a little. Here are some options:
At UQAM
•
...
• At UQAM
If you want to use the Intel compiler set:
module
...
load
...
openmpi/2.1.5-intel-19.0-mkl
...
module
...
load
...
utils/misc
...
# Only on CentOS 7 servers! To get an up to date version of cmake
cmake -DCOMPILER=intel
...
-DCMAKE_VERBOSE_MAKEFILE=ON
...
-DWORK_PREFIX=${MY_WORK_DIR} ${MY_GEM_DIR}
...
/project
...
• If you want to use the GNU compiler (gcc/gfortran) set:
module
...
load
...
openmpi/3.1.5-gcc-8.3
...
cmake
...
-DCOMPILER=gnu
...
-DCMAKE_VERBOSE_MAKEFILE=ON
...
-DWORK_PREFIX=${MY_WORK_DIR}
...
${MY_GEM_DIR}/project
On Beluga
module load intel/2019.3
module load openmpi
module load cmake/3.16.3
module load fftw-mpi
cmake -DCOMPILER=intel -DCMAKE_VERBOSE_MAKEFILE=ON -DWORK_PREFIX=${MY_WORK_DIR} ${MY_GEM_DIR}/project
On Niagara
•
...
• On Niagara using the native environment (recommended)
module
...
load
...
intel/2019u4
...
openmpi/4.0.1
...
fftw/3.3.8
...
cmake
...
cmake
...
-DCOMPILER=intel
...
-DCMAKE_VERBOSE_MAKEFILE=ON
...
-DWORK_PREFIX=${MY_WORK_DIR} ${MY_GEM_DIR}
...
/project
...
• On Niagara using the common Environmentenvironment
module
...
load
...
CCEnv
...
module
...
load
...
nixpkgs/16.09
...
module
...
load
...
intel/2019.3
...
module
...
load
...
openmpi
...
module
...
load
...
cmake/3.16.3
...
module
...
load
...
fftw-mpi
...
cmake
...
-DCOMPILER=intel
...
-DCMAKE_VERBOSE_MAKEFILE=ON
...
-DWORK_PREFIX=${MY_WORK_DIR} ${MY_GEM_DIR}
...
/project
...
Create executable
make
...
-j8
...
Run the model
...
work # When using the key '-jn', the make command will run 'n' makes in parallel. So in this case 8.
Note: Sometimes, when running make in parallel it does not compile the routines in the right order (especially after massive updates of the source code). In that case run the command without the key '-j8'.
Run GOAS
To run GOAS you need to change into the model work directory (replace the '...' in the following command!):
cd ${MY_WORK_DIR}
...
cd
...
work-...
...
# change into work directory, i.e.
...
work-linux26-x86-64-intel-19.0.3.199
...
Here you will find several example config files under 'configurations'. If you want to run, for example, a global YinYang simulation execute:
./runprep
...
-dircfg
...
configurations/GY_cfgs
...
./runmod
...
-dircfg
...
configurations/GY_cfgs
...
-ptopo
...
2x2x1
Changing the code
Before making any changes to the source code it is recommended to create a new branch, for example:
git checkout -b b_5.1-u1-climate
Once you change the source code follow the steps above, starting from "Set compiler version and compile".