ROMS-JEDI Compiling - Revision history

Arango: /* Compiling ROMS-JEDI Default Application WC13 */

2023-08-31T13:00:43Z

Compiling ROMS-JEDI Default Application WC13

← Older revision		Revision as of 13:00, 31 August 2023
Line 33:		Line 33:
	The strategy is to create a '''Bundle''' and '''build''' subdirectory for each '''ROMS-JEDI''' application. For '''WC13''' (default), we create '''Bundle_wc13''' and '''build_wc13''' below. Please follow the following steps to configure '''ROMS-JEDI''' in your computer:<div class="box"><span class="red">git clone <nowiki>https://github.com/JCSDA-internal/roms-jedi.git</nowiki></span> !> If the first time on your computer<br /><br /><span class="red">cd roms-jedi</span> !> ROMS-JEDI interface directory, <interface_dir><br /><span class="red">mkdir Bundle_wc13</span><br /><span class="red">cp bundle/.gitignore bundle/CMakeLists.txt Bundle_wc13</span><br /><span class="red">mkdir build_wc13</span><br /><span class="red">cd build_wc13</span><br /><br /><span class="red">ecbuild -DMPIEXEC_EXECUTABLE=$MPIRUN -DMPIEXEC_NUMPROC_FLAG="-n" -DCMAKE_BUILD_TYPE=Release ../Bundle_wc13</span><br /><span class="red">make -j 10</span><br /><br /><span class="red">cd roms-jedi</span> !> sub-directory: <interface_dir>/build_wc13/roms-jedi<br /><span class="red">ctest -N</span> !> lists all the Unit Tests available<br /><span class="red">ctest -E -V get_</span> !> runs all the Unit Tests<br /><br /><span class="red">cd test/Data</span> !> sub-directory: <interface_dir>/build_wc13/roms-jedi/test/Data<br /> !> to check the results in various sub-directories</div>		The strategy is to create a '''Bundle''' and '''build''' subdirectory for each '''ROMS-JEDI''' application. For '''WC13''' (default), we create '''Bundle_wc13''' and '''build_wc13''' below. Please follow the following steps to configure '''ROMS-JEDI''' in your computer:<div class="box"><span class="red">git clone <nowiki>https://github.com/JCSDA-internal/roms-jedi.git</nowiki></span> !> If the first time on your computer<br /><br /><span class="red">cd roms-jedi</span> !> ROMS-JEDI interface directory, <interface_dir><br /><span class="red">mkdir Bundle_wc13</span><br /><span class="red">cp bundle/.gitignore bundle/CMakeLists.txt Bundle_wc13</span><br /><span class="red">mkdir build_wc13</span><br /><span class="red">cd build_wc13</span><br /><br /><span class="red">ecbuild -DMPIEXEC_EXECUTABLE=$MPIRUN -DMPIEXEC_NUMPROC_FLAG="-n" -DCMAKE_BUILD_TYPE=Release ../Bundle_wc13</span><br /><span class="red">make -j 10</span><br /><br /><span class="red">cd roms-jedi</span> !> sub-directory: <interface_dir>/build_wc13/roms-jedi<br /><span class="red">ctest -N</span> !> lists all the Unit Tests available<br /><span class="red">ctest -E -V get_</span> !> runs all the Unit Tests<br /><br /><span class="red">cd test/Data</span> !> sub-directory: <interface_dir>/build_wc13/roms-jedi/test/Data<br /> !> to check the results in various sub-directories</div>

	The '''ecbuild''' command will clone the required '''JEDI''' components that are specified in '''Bundle_wc13/CMakeList.txt'''. For example:<div class="box"># Required repositories<br /><br /> ecbuild_bundle( PROJECT roms GIT "<nowiki>https://github.com/~~JCSDA-internal~~/~~roms_src~~.git</nowiki>" BRANCH ~~master~~ UPDATE )<br /> ecbuild_bundle( PROJECT oops GIT "<nowiki>https://github.com/jcsda-internal/oops.git</nowiki>" BRANCH develop UPDATE )<br /> ecbuild_bundle( PROJECT vader GIT "<nowiki>https://github.com/jcsda-internal/vader.git</nowiki>" BRANCH develop UPDATE )<br /> ecbuild_bundle( PROJECT saber GIT "<nowiki>https://github.com/jcsda-internal/saber.git</nowiki>" BRANCH develop UPDATE )<br /><br /> ecbuild_bundle( PROJECT gsw GIT "<nowiki>https://github.com/jcsda-internal/GSW-Fortran.git</nowiki>" BRANCH develop UPDATE )<br /> ecbuild_bundle( PROJECT ioda GIT "<nowiki>https://github.com/jcsda-internal/ioda.git</nowiki>" BRANCH develop UPDATE )<br /> ecbuild_bundle( PROJECT ufo GIT "<nowiki>https://github.com/jcsda-internal/ufo.git</nowiki>" BRANCH develop UPDATE )<br /><br /> ecbuild_bundle( PROJECT roms-jedi SOURCE ../ )</div>		The '''ecbuild''' command will clone the required '''JEDI''' components that are specified in '''Bundle_wc13/CMakeList.txt'''. For example:<div class="box"># Required repositories<br /><br /> ecbuild_bundle( PROJECT roms GIT "<nowiki>https://github.com/myroms/roms.git</nowiki>" BRANCH develop UPDATE )<br /> ecbuild_bundle( PROJECT oops GIT "<nowiki>https://github.com/jcsda-internal/oops.git</nowiki>" BRANCH develop UPDATE )<br /> ecbuild_bundle( PROJECT vader GIT "<nowiki>https://github.com/jcsda-internal/vader.git</nowiki>" BRANCH develop UPDATE )<br /> ecbuild_bundle( PROJECT saber GIT "<nowiki>https://github.com/jcsda-internal/saber.git</nowiki>" BRANCH develop UPDATE )<br /><br /> ecbuild_bundle( PROJECT gsw GIT "<nowiki>https://github.com/jcsda-internal/GSW-Fortran.git</nowiki>" BRANCH develop UPDATE )<br /> ecbuild_bundle( PROJECT ioda GIT "<nowiki>https://github.com/jcsda-internal/ioda.git</nowiki>" BRANCH develop UPDATE )<br /> ecbuild_bundle( PROJECT ufo GIT "<nowiki>https://github.com/jcsda-internal/ufo.git</nowiki>" BRANCH develop UPDATE )<br /><br /> ecbuild_bundle( PROJECT roms-jedi SOURCE ../ )</div>

	The '''ecbuild''' tool builds by default the '''RelWithDebInfo''' ('''-O2 -g''' options) for optimized with debugging information version of '''JEDI''' and '''ROMS-JEDI''', rendering slower execution. However, for faster and optimized execution, we include the directive '''-DCMAKE_BUILD_TYPE=Release''' to the '''ecbuild''' command. For debugging with TotalView, we include instead the directive '''-DCMAKE_BUILD_TYPE=Debug''', which is much slower.		The '''ecbuild''' tool builds by default the '''RelWithDebInfo''' ('''-O2 -g''' options) for optimized with debugging information version of '''JEDI''' and '''ROMS-JEDI''', rendering slower execution. However, for faster and optimized execution, we include the directive '''-DCMAKE_BUILD_TYPE=Release''' to the '''ecbuild''' command. For debugging with TotalView, we include instead the directive '''-DCMAKE_BUILD_TYPE=Debug''', which is much slower.

Arango: /* Compiling ROMS-JEDI Default Application WC13 */

2023-08-31T05:06:18Z

Compiling ROMS-JEDI Default Application WC13

← Older revision		Revision as of 05:06, 31 August 2023
Line 29:		Line 29:
	==Compiling ROMS-JEDI Default Application WC13==		==Compiling ROMS-JEDI Default Application WC13==

	By default, '''ROMS-JEDI''' is configured with a coarse (54x53x30 grid points) US West Coast ('''WC13''') application. See [[4DVar Tutorial Introduction]] for detailed information about the '''WC13''' configuration. However, any other ROMS application can be configured by including in the '''ecbuild''' command the directives '''`-~~DROMS_APP~~="MyAppCPP"`''' and '''-~~DROMS_APP_DIR~~="MyAppDirPath"'''.		By default, '''ROMS-JEDI''' is configured with a coarse (54x53x30 grid points) US West Coast ('''WC13''') application. See [[4DVar Tutorial Introduction]] for detailed information about the '''WC13''' configuration. However, any other ROMS application can be configured by including in the '''ecbuild''' command the directives '''-D<span class="twilightBlue">ROMS_APP</span>=MyAppCPP''' and '''-D<span class="twilightBlue">ROMS_APP_DIR</span>=MyAppDirPath'''.

	The strategy is to create a '''Bundle''' and '''build''' subdirectory for each '''ROMS-JEDI''' application. For '''WC13''' (default), we create '''Bundle_wc13''' and '''build_wc13''' below. Please follow the following steps to configure '''ROMS-JEDI''' in your computer:<div class="box"><span class="red">git clone <nowiki>https://github.com/JCSDA-internal/roms-jedi.git</nowiki></span> !> If the first time on your computer<br /><br /><span class="red">cd roms-jedi</span> !> ROMS-JEDI interface directory, <interface_dir><br /><span class="red">mkdir Bundle_wc13</span><br /><span class="red">cp bundle/.gitignore bundle/CMakeLists.txt Bundle_wc13</span><br /><span class="red">mkdir build_wc13</span><br /><span class="red">cd build_wc13</span><br /><br /><span class="red">ecbuild -DMPIEXEC_EXECUTABLE=$MPIRUN -DMPIEXEC_NUMPROC_FLAG="-n" -DCMAKE_BUILD_TYPE=Release ../Bundle_wc13</span><br /><span class="red">make -j 10</span><br /><br /><span class="red">cd roms-jedi</span> !> sub-directory: <interface_dir>/build_wc13/roms-jedi<br /><span class="red">ctest -N</span> !> lists all the Unit Tests available<br /><span class="red">ctest -E -V get_</span> !> runs all the Unit Tests<br /><br /><span class="red">cd test/Data</span> !> sub-directory: <interface_dir>/build_wc13/roms-jedi/test/Data<br /> !> to check the results in various sub-directories</div>		The strategy is to create a '''Bundle''' and '''build''' subdirectory for each '''ROMS-JEDI''' application. For '''WC13''' (default), we create '''Bundle_wc13''' and '''build_wc13''' below. Please follow the following steps to configure '''ROMS-JEDI''' in your computer:<div class="box"><span class="red">git clone <nowiki>https://github.com/JCSDA-internal/roms-jedi.git</nowiki></span> !> If the first time on your computer<br /><br /><span class="red">cd roms-jedi</span> !> ROMS-JEDI interface directory, <interface_dir><br /><span class="red">mkdir Bundle_wc13</span><br /><span class="red">cp bundle/.gitignore bundle/CMakeLists.txt Bundle_wc13</span><br /><span class="red">mkdir build_wc13</span><br /><span class="red">cd build_wc13</span><br /><br /><span class="red">ecbuild -DMPIEXEC_EXECUTABLE=$MPIRUN -DMPIEXEC_NUMPROC_FLAG="-n" -DCMAKE_BUILD_TYPE=Release ../Bundle_wc13</span><br /><span class="red">make -j 10</span><br /><br /><span class="red">cd roms-jedi</span> !> sub-directory: <interface_dir>/build_wc13/roms-jedi<br /><span class="red">ctest -N</span> !> lists all the Unit Tests available<br /><span class="red">ctest -E -V get_</span> !> runs all the Unit Tests<br /><br /><span class="red">cd test/Data</span> !> sub-directory: <interface_dir>/build_wc13/roms-jedi/test/Data<br /> !> to check the results in various sub-directories</div>

Robertson at 20:18, 30 August 2023

2023-08-30T20:18:53Z

← Older revision		Revision as of 20:18, 30 August 2023
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	<div class="title">Compiling ROMS-JEDI</div>		<div class="title">Compiling ROMS-JEDI</div>

			<!-- Edit Template:ROMS-JEDI_TOC to modify this Table of Contents-->
			<div style="float: left;margin: 0 20px 0 0;">{{ROMS-JEDI_TOC}}</div>__TOC__

			<div style="clear: both"></div>


	==Configuring GIT==		==Configuring GIT==

Robertson: Created page with "
Compiling ROMS-JEDI
==Configuring GIT== Before downloading the '''ROMS-JEDI''' repository, ensure that your '''~/.gitconfig''' has the appropriate '..."

2023-08-30T18:25:12Z

Created page with "<div class="title">Compiling ROMS-JEDI</div> ==Configuring GIT== Before downloading the '''ROMS-JEDI''' repository, ensure that your '''~/.gitconfig''' has the appropriate '..."

New page

<div class="title">Compiling ROMS-JEDI</div>

==Configuring GIT==

Before downloading the '''ROMS-JEDI''' repository, ensure that your '''~/.gitconfig''' has the appropriate '''git-lfs''' configuration for correctly downloading the default application (U.S. West Coast, '''WC13''' option) input and observation NetCDF files. Otherwise, the '''Unit Test Cases''' requiring input NetCDF files will fail. The '''Git LFS''' is a command line extension and specification for managing large files with '''Git'''. A sample of the configuration file looks like this:<div class="box">more ~/.gitconf [User] name = GivenName MiddleName FamilyName email = your@email [credential] helper = cache --timeout=7200 helper = store --file ~/.my-credentials [filter "lfs"] clean = git-lfs clean -- %f smudge = git-lfs smudge -- %f process = git-lfs filter-process required = true</div>

Alternatively, you may execute '''git lfs pull''' at your location of this repository to download a viable version of the '''Git LFS''' files from the remote repository in '''GitHub'''. Also, to automatically add the '''LFS''' filter to your existing '''~/.gitconfig''', you could use '''git lfs install''' from anywhere in your computer directories.

==Downloading ROMS-JEDI==

The '''ROMS-JEDI''' repository is private within the Joint Center for Satellite Data Assimilation ('''JCSDA''') community. Users need to be partners, contributors, or members of '''JCSDA''' to access all the '''JEDI''' components that are part of the abstract layer infrastructure centered around the Object Oriented Prediction System ('''OOPS''').

Use the following command to download the '''ROMS-JEDI''' interface:<div class="box">git clone <nowiki>https://github.com/JCSDA-internal/roms-jedi.git</nowiki></div>

==Requirements==

* Make sure you have the '''spack-stack''' software installed for either '''gfortran''' or '''ifort''' containing several packages need to run the '''ROMS-JEDI''' interface. For more information, please check https://github.com/JCSDA/spack-stack. In our computers at Rutgers University, the '''spack-stack''' can be loaded by executing either:<div class="box">module purge; module load stack-gcc; module list (gfortran compiler) module purge; module load stack-intel; module list (ifort compiler)</div>Installing the '''spack-stack''' is not trivial and requires computer software expertise.

* We also like to define the '''MPIRUN''' environmental variable to specify the '''MPI''' executable in a particular computer (say, '''srun''', '''mpirun''', etc.). We need the full path for '''ctest''' to work. Notice that we specify this executable in the '''ecbuild''' command below. For example:<div class="box">setenv MPIRUN /opt/slurm/bin/srun</div>

* Several environment variables can be activated for '''verbose debugging''' of the building blocks for the '''ROMS-JEDI''' interface: (use '''1''' or '''true''' to activate and '''0''' or '''false''' to deactivate)<div class="box">setenv LdebugGeometry 1 setenv LdebugAnalyticInit 1 setenv LdebugField 1 setenv LdebugFields 1 setenv LdebugFieldsUtils 1 setenv LdebugGeometry 1 setenv LdebugLinearModel 1 setenv LdebugLinearModel2Geovals 1 setenv LdebugModel 1 setenv LdebugModel2Geovals 1 setenv LdebugTrajectory 1</div>

==Compiling ROMS-JEDI Default Application WC13==

By default, '''ROMS-JEDI''' is configured with a coarse (54x53x30 grid points) US West Coast ('''WC13''') application. See [[4DVar Tutorial Introduction]] for detailed information about the '''WC13''' configuration. However, any other ROMS application can be configured by including in the '''ecbuild''' command the directives '''`-DROMS_APP="MyAppCPP"`''' and '''-DROMS_APP_DIR="MyAppDirPath"'''.

The strategy is to create a '''Bundle''' and '''build''' subdirectory for each '''ROMS-JEDI''' application. For '''WC13''' (default), we create '''Bundle_wc13''' and '''build_wc13''' below. Please follow the following steps to configure '''ROMS-JEDI''' in your computer:<div class="box">git clone <nowiki>https://github.com/JCSDA-internal/roms-jedi.git</nowiki> !> If the first time on your computer cd roms-jedi !> ROMS-JEDI interface directory, <interface_dir> mkdir Bundle_wc13 cp bundle/.gitignore bundle/CMakeLists.txt Bundle_wc13 mkdir build_wc13 cd build_wc13 ecbuild -DMPIEXEC_EXECUTABLE=$MPIRUN -DMPIEXEC_NUMPROC_FLAG="-n" -DCMAKE_BUILD_TYPE=Release ../Bundle_wc13 make -j 10 cd roms-jedi !> sub-directory: <interface_dir>/build_wc13/roms-jedi ctest -N !> lists all the Unit Tests available ctest -E -V get_ !> runs all the Unit Tests cd test/Data !> sub-directory: <interface_dir>/build_wc13/roms-jedi/test/Data !> to check the results in various sub-directories</div>

The '''ecbuild''' command will clone the required '''JEDI''' components that are specified in '''Bundle_wc13/CMakeList.txt'''. For example:<div class="box"># Required repositories ecbuild_bundle( PROJECT roms GIT "<nowiki>https://github.com/JCSDA-internal/roms_src.git</nowiki>" BRANCH master UPDATE ) ecbuild_bundle( PROJECT oops GIT "<nowiki>https://github.com/jcsda-internal/oops.git</nowiki>" BRANCH develop UPDATE ) ecbuild_bundle( PROJECT vader GIT "<nowiki>https://github.com/jcsda-internal/vader.git</nowiki>" BRANCH develop UPDATE ) ecbuild_bundle( PROJECT saber GIT "<nowiki>https://github.com/jcsda-internal/saber.git</nowiki>" BRANCH develop UPDATE ) ecbuild_bundle( PROJECT gsw GIT "<nowiki>https://github.com/jcsda-internal/GSW-Fortran.git</nowiki>" BRANCH develop UPDATE ) ecbuild_bundle( PROJECT ioda GIT "<nowiki>https://github.com/jcsda-internal/ioda.git</nowiki>" BRANCH develop UPDATE ) ecbuild_bundle( PROJECT ufo GIT "<nowiki>https://github.com/jcsda-internal/ufo.git</nowiki>" BRANCH develop UPDATE ) ecbuild_bundle( PROJECT roms-jedi SOURCE ../ )</div>

The '''ecbuild''' tool builds by default the '''RelWithDebInfo''' ('''-O2 -g''' options) for optimized with debugging information version of '''JEDI''' and '''ROMS-JEDI''', rendering slower execution. However, for faster and optimized execution, we include the directive '''-DCMAKE_BUILD_TYPE=Release''' to the '''ecbuild''' command. For debugging with TotalView, we include instead the directive '''-DCMAKE_BUILD_TYPE=Debug''', which is much slower.

==Compiling other ROMS-JEDI Applications==

Any '''ROMS''' application can be run in '''ROMS-JEDI''' by specifying the appropriate CPP option and necessary input files. Only '''WC13''' is provided with the interface. However, we facilitate how to run such applications. Notice that the '''WC13''' configuration and input files are located in '''roms-jedi/test/Applications/wc13'''. The template input YAML files are located '''roms-jedi/test/templates'''. We use a '''Perl''' script to create the application input YAML files from the templates. Please check in '''roms-jedi/test/Applications/wc13/testinput'''.

For example, if running the U.S. East Coast '''DOPPIO''' application (240x104x40 grid points) or any other, please follow the following steps to configure '''ROMS-JEDI''':<div class="box">cd roms-jedi !> ROMS-JEDI interface directory, <interface_dir> mkdir Bundle_doppio cp bundle/.gitignore bundle/CMakeLists.txt Bundle_doppio mkdir build_doppio cd build_doppio ecbuild -DMPIEXEC_EXECUTABLE=$MPIRUN -DMPIEXEC_NUMPROC_FLAG="-n" -DROMS_APP="DOPPIO" \ -DROMS_APP_DIR="DOPPIOpath" -DCMAKE_BUILD_TYPE=Release ../Bundle_doppio make -j 10 cd roms-jedi !> sub-directory: <interface_dir>/build_doppio/roms-jedi ctest -N !> lists all the Unit Tests available ctest -E -V get_ !> runs all the Unit Test cd test/Data !> sub-directory: <interface_dir>/build_doppio/roms-doppio/test/Data !> to check the results in various sub-directories</div>

ROMS-JEDI Compiling - Revision history

Arango: /* Compiling ROMS-JEDI Default Application WC13 */

Arango: /* Compiling ROMS-JEDI Default Application WC13 */

Robertson at 20:18, 30 August 2023

Robertson: Created page with "Compiling ROMS-JEDI ==Configuring GIT== Before downloading the '''ROMS-JEDI''' repository, ensure that your '''~/.gitconfig''' has the appropriate '..."

Robertson: Created page with "
Compiling ROMS-JEDI
==Configuring GIT== Before downloading the '''ROMS-JEDI''' repository, ensure that your '''~/.gitconfig''' has the appropriate '..."