GEOS GCM Fixture
CI Status
| CI Provider | Status |
|---|---|
| CircleCI |  |
| AWS CodeBuild |  |
| GitHub |  |
Current State of GEOSgcm Subrepos
How to build GEOS GCM
Preliminary Steps
Load Build Modules
In your .bashrc or .tcshrc or other rc file add a line:
NCCS
NCCS currently has two different OSs. So you'll need to use different modulefiles depending on which OS you are using.
SLES 12
module use -a /discover/swdev/gmao_SIteam/modulefiles-SLES12SLES 15
module use -a /discover/swdev/gmao_SIteam/modulefiles-SLES15NAS
module use -a /nobackup/gmao_SIteam/modulefilesGMAO Desktops
On the GMAO desktops, the SI Team modulefiles should automatically be
part of running module avail but if not, they are in:
module use -a /ford1/share/gmao_SIteam/modulefilesAlso do this in any interactive window you have. This allows you to get module files needed to correctly checkout and build the model.
Now load the GEOSenv module:
module load GEOSenvwhich obtains the latest git, CMake, and mepo modules.
Obtain the Model
On GitHub, there are three ways to clone the model: SSH, HTTPS, or GitHub CLI.
The first two are "git protocols" which determine how git communicates with
GitHub: either through https or ssh. (The latter is a CLI that uses either ssh or
https protocol underneath.)
For developers of GEOS, the SSH git protocol is recommended as it can avoid some issues if two-factor authentication (2FA) is enabled on GitHub.
SSH
To clone the GEOSgcm using the SSH url (starts with git@github.com), you run:
git clone -b vX.Y.Z git@github.com:GEOS-ESM/GEOSgcm.gitwhere vX.Y.Z is a tag from a GEOSgcm release. Note if you don't use -b, you will get the main branch and that can change from day-to-day.
Permission denied (publickey)
If this is your first time using GitHub with any SSH URL, you might get this error:
Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.If you do see this, you need to upload an ssh key to your GitHub account. This needs to be done on any machine that you want to use the SSH URL through.
HTTPS
To clone the model through HTTPS you run:
git clone -b vX.Y.Z https://github.com/GEOS-ESM/GEOSgcm.gitwhere vX.Y.Z is a tag from a GEOSgcm release. Note if you don't use -b, you will get the main branch and that can change from day-to-day.
Note that if you use the HTTPS URL and have 2FA set up on GitHub, you will need to use personal access tokens as a password.
GitHub CLI
You can also use the GitHub CLI with:
gh repo clone GEOS-ESM/GEOSgcm -- -b vX.Y.Zwhere vX.Y.Z is a tag from a GEOSgcm release. Note if you don't use -b, you will get the main branch and that can change from day-to-day.
Note that when you first use gh, it will ask what your preferred git protocol
is (https or ssh) to use "underneath". The caveats above will apply to whichever
you choose.
Single Step Building of the Model
If all you wish is to build the model, you can run parallel_build.csh from a head node. Doing so will checkout all the external repositories of the model and build it. When done, the resulting model build will be found in build/ and the installation will be found in install/ with setup scripts like gcm_setup and fvsetup in install/bin.
Building at NCCS (Multiple OSs)
In all the examples below, NCCS builds will act differently. Because NCCS currently has two different OSs, when you use
parallel_build.csh you will see that the build and install directories will be appended with -SLES12 or -SLES15 depending
on where you submitted to. When NCCS moves to a single OS again, this will be removed.
Note that if you use the -builddir and -installdir options, you can override this behavior and no OS will be automatically
appended.
Develop Version of GEOS GCM
parallel_build.csh provides a special flag for checking out the
development branches of GEOSgcm_GridComp, GEOSgcm_App, GMAO_Shared, and GEOS_Util. If you run:
parallel_build.csh -developthen mepo will run:
mepo develop GEOSgcm_GridComp GEOSgcm_App GMAO_Shared GEOS_UtilDebug Version of GEOS GCM
To obtain a debug version, you can run parallel_build.csh -debug which will build with debugging flags. This will build in build-Debug/ and install into install-Debug/.
Do not create and install source tarfile with parallel_build
Note that running with parallel_build.csh will create and install a tarfile of the source code at build time. If you wish to avoid
this, run parallel_build.csh with the -no-tar option.
Passing additional CMake options to parallel_build.csh
While parallel_build.csh has many options, it does not cover all possible CMake options possible in GEOSgcm. If you wish to
pass additional CMake options to parallel_build.csh, you can do so by using -- and then the CMake options. Note that anything
after the -- will be interpreted as a CMake option, which could lead to build issues if not careful.
For example, if you want to build a develop Debug build on Cascade Lake while turning on StratChem reduced mechanism and the CODATA 2018 options:
parallel_build.csh -develop -debug -cas -- -DSTRATCHEM_REDUCED_MECHANISM=ON -DUSE_CODATA_2018_CONSTANTS=ONAs noted above all the "regular" parallel_build.csh options must be listed before the -- flag.
Multiple Steps for Building the Model
The steps detailed below are essentially those that parallel_build.csh performs for you. Either method should yield identical builds.
Mepo
The GEOS GCM is comprised of a set of sub-repositories. These are
managed by a tool called mepo. To
clone all the sub-repos, you can run mepo clone inside the fixture:
cd GEOSgcm
mepo cloneThe first command initializes the multi-repository and the second one
clones and assembles all the sub-repositories according to
components.yaml
Checking out develop branches of GEOSgcm_GridComp, GEOSgcm_App, GMAO_Shared, and GEOS_Util
To get development branches of GEOSgcm_GridComp, GEOSgcm_App, GMAO_Shared, and GEOS_Util (a la
the -develop flag for parallel_build.csh, one needs to run the
equivalent mepo command. As mepo itself knows (via components.yaml) what the development branch of each
subrepository is, the equivalent of -develop for mepo is to
checkout the development branches of GEOSgcm_GridComp, GEOSgcm_App, GMAO_Shared, and GEOS_Util:
mepo develop GEOSgcm_GridComp GEOSgcm_App GMAO_Shared GEOS_UtilThis must be done after mepo clone as it is running a git command in
each sub-repository.
Build the Model
Load Compiler, MPI Stack, and Baselibs
On tcsh:
source @env/g5_modulesor on bash:
source @env/g5_modules.shCreate Build Directory
We currently do not allow in-source builds of GEOSgcm. So we must make a directory:
mkdir buildThe advantages of this is that you can build both a Debug and Release version with the same clone if desired.
Run CMake
CMake generates the Makefiles needed to build the model.
cd build
cmake .. -DBASEDIR=$BASEDIR/Linux -DCMAKE_Fortran_COMPILER=ifort -DCMAKE_INSTALL_PREFIX=../installThis will install to a directory parallel to your build directory. If you prefer to install elsewhere change the path in:
-DCMAKE_INSTALL_PREFIX=<path>and CMake will install there.
Create and install source tarfile
Note that running with parallel_build.csh will create and install a tarfile of the source code at build time. But if CMake is run by hand, this is not the default action (as many who build with CMake by hand are developers and not often running experiments). In order to enable this at install time, add:
-DINSTALL_SOURCE_TARFILE=ONto your CMake command.
Build and Install with Make
make -jN installwhere N is the number of parallel processes. On discover head nodes, this should only be as high as 2 due to limits on the head nodes. On a compute node, you can set N has high as you like, though 8-12 is about the limit of parallelism in our model's make system.
Run the GCM
Once the model has built successfully, you will have an install/ directory in your checkout. To run gcm_setup go to the install/bin/ directory and run it there:
cd install/bin
./gcm_setupContributing
Please check out our contributing guidelines.
License
All files are currently licensed under the Apache-2.0 license, see LICENSE.
Previously, the code was licensed under the NASA Open Source Agreement, Version 1.3.