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Merge pull request #5 from uramirez8707/gh_2021.02
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| *~ | ||
| *.o | ||
| *.mod | ||
| *.s | ||
| *.out | ||
| pathnames* | ||
| /*.zip | ||
| /*.tar.gz | ||
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| Makefile | ||
| # From https://github.com/github/gitignore/blob/master/Autotools.gitignore | ||
| # http://www.gnu.org/software/automake | ||
| Makefile.in | ||
| /ar-lib | ||
| /mdate-sh | ||
| /py-compile | ||
| /test-driver | ||
| /tap-driver.sh | ||
| /ylwrap | ||
| *.log | ||
| *.trs | ||
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| # http://www.gnu.org/software/autoconf | ||
| autom4te.cache | ||
| /autoscan.log | ||
| /autoscan-*.log | ||
| /aclocal.m4 | ||
| /compile | ||
| /config.guess | ||
| /config.h.in | ||
| /config.log | ||
| /config.status | ||
| /config.sub | ||
| /configure | ||
| /configure.scan | ||
| /depcomp | ||
| /install-sh | ||
| /missing | ||
| /stamp-h1 | ||
| .deps | ||
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| # https://www.gnu.org/software/libtool/ | ||
| libtool | ||
| /ltmain.sh | ||
| *.lo | ||
| *.la | ||
| .libs | ||
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| # http://www.gnu.org/software/texinfo | ||
| /texinfo.tex | ||
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| # http://www.gnu.org/software/m4/ | ||
| m4/libtool.m4 | ||
| m4/ltoptions.m4 | ||
| m4/ltsugar.m4 | ||
| m4/ltversion.m4 | ||
| m4/lt~obsolete.m4 | ||
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| .dirstamp |
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| before_script: | ||
| - hostname | ||
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| .ncrc_build: &ncrc_build | ||
| script: | ||
| - source /opt/cray/pe/modules/default/init/bash | ||
| - module rm cray-netcdf cray-hdf5 PrgEnv-intel PrgEnv-pgi PrgEnv-gnu PrgEnv-cray | ||
| - module load PrgEnv-${COMPILER_FAMILY} | ||
| - module swap ${COMPILER_NAME} ${COMPILER_NAME}/${COMPILER_VERSION} | ||
| - module load cray-hdf5 cray-netcdf | ||
| - mkdir local | ||
| - git clone https://github.com/NOAA-GFDL/FMS.git FMS | ||
| - cd FMS | ||
| - autoreconf --install | ||
| - ./configure --prefix=${CI_BUILDS_DIR}/local | ||
| - make | ||
| - make install | ||
| - cd .. | ||
| - autoreconf --install | ||
| - ./configure | ||
| - make | ||
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| build:ncrc:intel19:debug: | ||
| stage: build | ||
| tags: | ||
| - ncrc | ||
| variables: | ||
| CC: cc | ||
| COMPILER_FAMILY: intel | ||
| COMPILER_NAME: intel | ||
| COMPILER_VERSION: 19.0.5.281 | ||
| FC: ftn | ||
| F77: ftn | ||
| FCFLAGS: "-I${CI_BUILDS_DIR}/local/include -O0" | ||
| FFLAGS: "-I${CI_BUILDS_DIR}/local/include -O0" | ||
| LDFLAGS: "-L${CI_BUILDS_DIR}/local/lib" | ||
| <<: *ncrc_build | ||
| artifacts: | ||
| paths: | ||
| - .libs/libatmos_phys.so | ||
| - ./*.mod |
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| # atmos_phys | ||
| This is the repository that combines the atmosphere physics and chemistry | ||
| ## Table of contents | ||
| * [Guidelines for Contributing](README.md#guidelines-for-contributing) | ||
| * [Instructions on merging in code from atmos_param or atmos_shared](README.md#instructions-on-merging-in-code-from-atmos_param-or-atmos_shared) | ||
| * [XML changes to checkout atmos_phys](README.md#xml-changes-to-checkout-atmos_phys) | ||
| ## Guidelines for Contributing | ||
| If you have code you would like to contribute, you will first create a git branch. | ||
| Your branch should be in the format of /user/**ini**/**BranchName** where **ini** | ||
| are your initals and **BranchName** is a name that describes the purpose of your | ||
| branch. Avoid using a BranchName like *bugfix* or *update* because this is not | ||
| descritive. | ||
| ```bash | ||
| git checkout -b user/ini/BranchName | ||
| ``` | ||
| Second, you will commit your changes, and push them to the atmos_phys remote | ||
| repository. | ||
| ```bash | ||
| git push -u origin user/ini/BranchName | ||
| ``` | ||
| After the changes are pushed, you can share your code with others. If your code | ||
| should be included in the main model development, you can submit a merge request by | ||
| clicking on the Merge Requests link on the gitlab page. Please include a detailed | ||
| description of the changes made by your branch. You should submit the merge to the | ||
| main development branch (*master*). Assign your merge request to Uriel Ramirez. | ||
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| ## Instructions on merging in code from atmos_param or atmos_shared | ||
| In order to commit changes that currently exist on atmos_param or atmos_shared, | ||
| you first have to commit and push the changes to a branch in the repository you are | ||
| working in. Next you will clone atmos_phys. After that, you will add the original | ||
| repository to as a remote in your atmos_phys directory. You can then fetch from the | ||
| original repository and merge in the branch you were working on. | ||
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| Below is an example set of instructions to accomplish this. This assumes that you | ||
| cloned atmos_param. | ||
| ```bash | ||
| git clone https://gitlab.gfdl.noaa.gov/fms/atmos_phys.git #clone atmos_param | ||
| cd atmos_phys | ||
| pushd ../atmos_param/ #Set up a directory stack with the two repo directories | ||
| git checkout user/ter/exampleBranch #check out your user branch | ||
| git fetch #fetch any changes that may have occurred in atmos_param since you branched | ||
| git pull origin/master #merge in the master (update your code base) | ||
| ## The following 3 lines can be skipped if you already have committed changes ## | ||
| touch test.file #Make your changes (DO NOT COPY THIS, it is just an example) | ||
| git add test.file #stage your changes | ||
| git commit -m "Save a test commit to user branch" #commit your changes | ||
| ## The folowing can be skipped if you have already pushed your changes ## | ||
| git push -u origin user/ter/exampleBranch | ||
| pushd #change directory to the atmos_phys folder | ||
| git checkout -b user/ter/exampleBranch #create your branch in atmos_phys | ||
| git remote add param https://gitlab.gfdl.noaa.gov/fms/atmos_param.git #add atmos_param as a remote | ||
| git fetch param #fetch the contents of the atmos_param | ||
| git merge param/user/ter/exampleBranch #merge your branch from atmos_param into your branch on atmos_phys | ||
| git push -u origin user/ter/exampleBranch | ||
| ``` | ||
| A note on git remotes: | ||
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| The default name for a remote is **origin**. When you clone a repository, the remote | ||
| is automatically given the name **origin**. When you add a remote, you can name it | ||
| anything except origin. In the above example, I named the remote **param**. That's | ||
| why I fetch from **param**. To see what remotes you have set up, you can issue the | ||
| command | ||
| ```bash | ||
| git remote -v | ||
| ``` | ||
|
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| ## XML changes to checkout atmos_phys | ||
| There are a few modifications to an XML in order switch to the atmos_phys code. | ||
| An XML will have a section in the compile experiment that looks like the following: | ||
| ```xml | ||
| <component name="atmos_phys" requires="fms" paths="atmos_param atmos_shared"> | ||
| <description domainName="" communityName="" communityVersion="$(RELEASE)" communityGrid=""/> | ||
| <source versionControl="git" root="http://gitlab.gfdl.noaa.gov/fms"> | ||
| <codeBase version="$(RELEASE)"> atmos_shared.git atmos_param.git </codeBase> | ||
| <csh><![CDATA[ | ||
| ( cd atmos_shared && git checkout $(ATMOS_GIT_TAG) ) | ||
| ( cd atmos_param && git checkout $(ATMOS_GIT_TAG) ) | ||
| ]]> | ||
| </csh> | ||
| </source> | ||
| <compile> | ||
| <cppDefs>$(F2003_FLAGS) -DCLUBB</cppDefs> | ||
| </compile> | ||
| </component> | ||
| ``` | ||
| This can be found by searching the XML for *atmos_phys* or *atmos_shared.git* or | ||
| *atmos_param.git*. This <component> block should be updated to the following: | ||
| ```xml | ||
| <component name="atmos_phys" requires="fms" paths="atmos_phys"> | ||
| <description domainName="" communityName="" communityVersion="$(RELEASE)" communityGrid=""/> | ||
| <source versionControl="git" root="http://gitlab.gfdl.noaa.gov/fms"> | ||
| <codeBase version="$(RELEASE)"> atmos_phys.git </codeBase> | ||
| <csh><![CDATA[ | ||
| ( cd atmos_phys && git checkout $(ATMOS_GIT_TAG) ) | ||
| ]]> | ||
| </csh> | ||
| </source> | ||
| <compile> | ||
| <cppDefs>$(F2003_FLAGS) -DCLUBB</cppDefs> | ||
| </compile> | ||
| </component> | ||
| ``` | ||
| 1. The **paths** has been changed from "atmos_param atmos_shared" to "atmos_phys". | ||
| 2. The **codeBase** was changed from **atmos_shared.git atmos_param.git** to **atmos_phys.git** | ||
| 3. The `csh` block was updated to only `cd` to atmos_phys | ||
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| NOTE: Users should switch to atmos_phys if they are checking out code that is newer | ||
| than xanadu. If your model is running code older than xanadu, you should check the | ||
| code out from atmos_shared and atmos_param. |
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