Difference between revisions of "Compiling GCHP"

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'''''[[Setting Up the GCHP Environment|Previous]] | [[GCHP_Basic_Example_Run|Next]] | [[Getting_Started_With_GCHP|User Manual Home]] | [[GEOS-Chem_HP|GCHP Home]]'''''
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----
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<span style="color:crimson;font-size:120%">'''The GCHP documentation has moved to https://gchp.readthedocs.io/.''' The GCHP documentation on http://wiki.seas.harvard.edu/ will stay online for several months, but it is outdated and no longer active!</span>
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----
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'''''[[Downloading_GCHP|Previous]] | [[Obtaining_a_GCHP_Run_Directory|Next]] | [[Getting Started with GCHP]] | [[GCHP Main Page]]'''''
 
#[[GCHP_Hardware_and_Software_Requirements|Hardware and Software Requirements]]
 
#[[GCHP_Hardware_and_Software_Requirements|Hardware and Software Requirements]]
#[[Downloading_GCHP|Downloading Source Code]]
 
#[[Obtaining_a_GCHP_Run_Directory|Obtaining a Run Directory]]
 
 
#[[Setting_Up_the_GCHP_Environment|Setting Up the GCHP Environment]]
 
#[[Setting_Up_the_GCHP_Environment|Setting Up the GCHP Environment]]
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#[[Downloading_GCHP|Downloading Source Code and Data Directories]]
 
#<span style="color:blue">'''Compiling'''</span>
 
#<span style="color:blue">'''Compiling'''</span>
#[[GCHP_Basic_Example_Run|Basic Example Run]]
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#[[Obtaining_a_GCHP_Run_Directory|Obtaining a Run Directory]]
#[[Running_GCHP|Configuring a Run]]
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#[[Running_GCHP:_Basics|Running GCHP: Basics]]
#[[GEOS-Chem_HP_Output_Data|Output Data]]
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#[[Running_GCHP:_Configuration|Running GCHP: Configuration]]
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#[[GCHP_Output_Data|Output Data]]
 
#[[Developing_GCHP|Developing GCHP]]
 
#[[Developing_GCHP|Developing GCHP]]
 
#[[GCHP_Run_Configuration_Files|Run Configuration Files]]
 
#[[GCHP_Run_Configuration_Files|Run Configuration Files]]
 
<br>
 
<br>
  
== Overview ==
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Compiling GCHP is the same procedure as compiling GEOS-Chem Classic. Please see [http://wiki.seas.harvard.edu/geos-chem/index.php/Compiling_with_CMake Compiling with CMake] for instructions.
 
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This section provides instructions on how to clean and compile GCHP. There are several options for cleaning and compiling which allow clean and compilation of subsets of modules, thereby minimizing recompilation to only modules you have modified.
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You are ready to compile GCHP after you have obtained the GCHP source code, set up your run directory, and set your environment. First time compilation can take a while (30 minutes or more) because it requires building large modules, including [https://www.earthsystemcog.org/projects/esmf/ ESMF], [https://geos5.org/wiki/index.php?title=MAPL_software MAPL], [https://www.gfdl.noaa.gov/fv3/ FV3 dycore advection], and GEOS-Chem. MAPL, which is short for Modeling, Analysis and Prediction Layer, is built on ESMF, aka the Earth System Modeling Framework. Both systems are highly flexible but highly complex, with significant compilation times. Fortunately, MAPL and ESMF do not need to be recompiled unless parts of their code have been modified which is usually not necessary. Subsequent compile times will therefore be significantly shorter, on the same order of magnitude as compiling GEOS-Chem Classic.
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== Initial Compilation ==
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To compile GCHP from scratch, navigate to your run directory and check that your <tt>gchp.env</tt> symbolic link is pointing to the environment file you wish to use. Next, type the following within the run directory:
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make clean
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make build
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These command will execute <tt>./build.sh clean</tt> and <tt>./build.sh build</tt>. All build information is sent to both the terminal window and to a log file called <tt>compile.log</tt>. Git information for both source code repositories at compile time are recorded in a separate file called <tt>lastbuild</tt> for future reference. Upon successful compilation, the following empty files are created in your GCHP source code directories:
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* <tt>GCHP/ESMF/esmf.install</tt>
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* <tt>GCHP/Shared/mapl.install</tt>
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* <tt>GCHP/FVdycoreCubed_GridComp/fvdycore.install</tt>
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These files indicate successful compilation per module and their presence prompts the GCHP source code <tt>Makefile</tt> to skip compiling each component during future builds unless you explicitly clean the source code. If you are ever uncertain on whether your ESMF, MAPL, and FV3 dycore were previously build, check if these files exist.
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== Subsequent Compilation ==
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For subsequent GCHP compilations you have several options. You can see all options by typing the following at the prompt from within your run directory:
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make help
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This will display all make options to your screen. For compilation the make targets you are interested in are clean, clean_mapl, clean_gc, build, build_mapl, and build_gc. Here is a brief summary of these options.
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Clean/compile ALL source code, including ESMF, MAPL, and FV3:
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make clean
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make build
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Clean/compile all source code except ESMF:
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make clean_mapl
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make build_mapl
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Clean/compile all source code except ESMF, MAPL, and FV3:
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make clean_gc
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make build_gc
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Same as above but compile GEOS-Chem with debug flags turned on (note that this will slow down the model)
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make build_gc_debug
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A typical workflow would look like you getting a run directory, compiling from scratch (make clean; make compile), editing GEOS-Chem code in GeosCore, and then recompiling without cleaning (make build_gc). Since this workflow is the most common the default make target, meaning the target used when none is specified, is set to build_gc. Therefore to rebuild GEOS-Chem after changing GEOS-Chem files or any high-level files in the GCHP directory you can simply type this:
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make
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Note that if you change your underlying libraries set in your environment you MUST do a full source code clean before rebuilding. Otherwise you will likely encounter a segmentation fault when running the model. For this reason it is recommended that you create a new run directory for each new environment you want to run in, e.g. if you want to test with both Intel and GNU fortran compilers.
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Also note that these build targets were added in GCHP version 12.2.0. If you are using an earlier version type <tt>make help</tt> to view your make options.
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== Checking for Successful Compilation ==
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If GCHP compiled without issues, you should see:
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###################################
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### GCHP compiled successfully! ###
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###################################
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Compiling GCHP produces a GCHP executable called <tt>geos</tt> that is stored in the <tt>bin/</tt> sub-directory of your GEOS-Chem source code directory. Compiling within the run directory makes a copy of the executable locally for easy use. This copy is what you should use when you run.
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Compiler output, including warnings and error messages, will be stored in a log file called <tt>compile.log</tt>. If you inspect your log file or watch the compile output real-time, you will notice that there are many warnings and error messages. Many of these errors are due to leftover components in MAPL which are no longer used but which still try to compile. As long as the compilation continues, these errors can almost always be ignored and they will have no effect on the operation of GCHP.
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Beware that once you have an executable you must not rename your run directory or your source code directory or the executable will no longer work. This is because the GCHP executable will include paths to ESMF libraries that incorporate the <tt>CodeDir</tt> symbolic link in the run directory path. However, you can copy the executable elsewhere for use. If you do this then it is also a good idea to also copy <tt>lastbuild</tt> and <tt>compile.log</tt> to your new run directory to keep track of where your executable came from. If you encounter an error while running GCHP that an ESMF shared library is missing, check that the exact path in the error message is still valid.
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If you run into problems please contact the GEOS-Chem Support Team for help.
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== Using Debug Flags ==
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After the initial compilation you may turn on debug flags for debugging subsequent compilations of GEOS-Chem code. Do this with the following make option:
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make compile_debug
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Be aware that turning on debug flags will slow down your run. Just as for GEOS-Chem Classic, you should always recompile GCHP without debug flags prior to doing production runs.
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== Additional Makefile Options ==
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The GCHP run directory <tt>Makefile</tt> contains several options for cleaning and compiling GCHP as well as other functionalities. Options are printed out by typing the following at the command line:
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make help
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This will output something like this to your screen.
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%%%    GCHP Run Directory Makefile Options    %%%
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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Usage: make TARGET [OPTIONAL-FLAGS]
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Default threads for compiling is hard-coded as 6
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----------------------------------------------------------
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TARGET may be one of the following:
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----------------------------------------------------------
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To print settings to screen:
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  printbuildinfo  Print out git info for GC and GCHP repos
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  help            If you got this far, you know this one
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To clean source code:
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  clean_all        Clean all source code using build.sh
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  clean_gc        Clean GEOS-Chem classic only using build.sh
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  clean_mapl      Clean MAPL and FVdyCore using build.sh
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  clean_nuclear    Clean everything using build.sh
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  superclean      Remove exe, logs, output, and clean ALL code
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To compile:
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  compile_clean    Include everything
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  compile_standard  Skip MAPL, FvDyCore, and ESMF; debug off
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  compile_debug    Skip MAPL, FvDyCore, and ESMF; debug on
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  compile_mapl      Skip ESMF
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To remove run directory files:
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  cleanup_output  Remove output data, log files, and executable
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  cleanup_data    Remove output data
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  cleanup_logs    Remove log files
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  cleanup_exe      Remove executable
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To run interactively:
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  run_interactive
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To clean, build, and run interactively:
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  gchp_clean      Include everything
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  gchp_standard    Skip MAPL, FvDyCore, and ESMF; debug off
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  gchp_debug      Skip MAPL, FvDyCore, and ESMF; debug on
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  gchp_mapl        Skip ESMF
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Some very useful options include the following:
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*'''''<tt>make printbuildinfo</tt>:''''' prints git information such as branch and last commit for the GEOS-Chem and GCHP repositories your <tt>CodeDir</tt> symbolic link points to.
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*'''''<tt>make cleanup_output</tt>:''''' cleans your run directory to remove all traces of your last run, including log and output files, but will not remove your executable or last build information.
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== Advanced Compilation Topics ==
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The <tt>Makefile</tt> in the run directory invokes a bash shell script called <tt>build.sh</tt> that includes changing into the source code directory and invoking source code Makefiles. This section details the capabilities of <tt>build.sh</tt> and source code <tt>make</tt> options for advanced users who wish to better understand how GCHP works. You may skip this section and return to it at a later date when you want to dive deeper into how GCHP is compiled.
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=== build.sh ===
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Whenever <tt>build.sh</tt> is executed it first checks if you have set up your environment. If it is not then you will be prompted to do this.  If you have multiple terminal windows and cannot remember if you have loaded your environment, a quick check is to execute the <tt>help</tt> option of <tt>build.sh</tt>.
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./build.sh help
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If you have set up your environment then clean and compile options of <tt>build.sh</tt> will print to screen. For example, when working on the Harvard Odyssey compute cluster you output will look as follows:
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MPI_ROOT is to /n/sw/fasrcsw/apps/Comp/intel/15.0.0-fasrc01/mvapich2/2.2-fasrc01
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Script name:
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  build.sh
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Arguments:
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  Accepts single argument indicating clean and/or compile settings.
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  Currently implemented arguments include:
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      clean_gc        - classic only
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      clean_nuclear    - GCHP, ESMF, MAPL, FVdycore (be careful!)
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      clean_all        - classic, GCHP, ESMF, MAPL, FVdycore (be careful!)
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      clean_mapl      - mapl and fvdycore only
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      compile_debug    - turns on debug flags, no cleaning
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      compile_standard - no cleaning
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      compile_mapl    - includes fvdycore
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      compile_clean    - cleans and compiles everything (be careful!)
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Example usage:
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  ./build.sh compile_standard
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The default compile commands for <tt>compile_clean</tt>, <tt>compile_standard</tt>, and <tt>compile_mapl</tt> are defined in <tt>build.sh</tt> as:
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    make -j${SLURM_NTASKS} NC_DIAG=y  CHEM=standard EXTERNAL_GRID=y  \
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                          DEBUG=y    DEVEL=y      TRACEBACK=y      \
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                          MET=geos-fp GRID=4x5      NO_REDUCED=y      \
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                          UCX=n      hpc
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The compile command for <tt>compile_debug</tt> is the same as above with <tt>BOUNDS=yes</tt> and <tt>FPEX=yes</tt> added.
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=== Source Code Makefiles ===
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At its core, building GCHP simply requires the inclusion of an additional option, <tt>HPC=yes</tt>, in the source code directory make command beyond what is typically included in GEOS-Chem compilation. Appending <tt>HPC=yes</tt> causes the make procedure to look for the contents of GCHP, and bypasses much of the serial GEOS-Chem code. For example, base GEOS-Chem classic source code is cleaned using the following command:
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make HPC=yes realclean
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After the process completes, the <tt>GCHP/</tt> subdirectory is completely cleaned by changing into that directory and doing:
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make EXTERNAL_GRID=yes the_nuclear_option
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Calling <tt>make</tt> with <tt>the_nuclear_option</tt> defined in <tt>GCHP/Makefile</tt> removes ''all'' compiled code in the directory. As implied by the name, this is not to be used lightly! The nuclear option is an alias, calling three commands in turn: <tt>wipeout_esmf</tt>, <tt>wipeout_mapl</tt>, and <tt>wipeout_fvdycore</tt>. 
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If you are interested in seeing the core <tt>make</tt> commands used for all options provided in the run directory <tt>Makefile</tt>, see the commands defined in <tt>build.sh</tt>. You can then trace the build sequence by looking at the Makefiles in the GEOS-Chem and GCHP repositories. Note that calling <tt>make</tt> always invokes the <tt>Makefile</tt> in the directory you are in and changing into the GEOS-Chem and GCHP source code directories occurs within <tt>build.sh</tt>. Also note that the <tt>GRID=4x5</tt> argument has no effect on the resolution at which the model runs since GCHP functions on the cubed-sphere grid. However, passing <tt>GRID</tt> is required so that components of GEOS-Chem Classic are functional.
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--------------------------------------
 
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'''''[[Setting Up the GCHP Environment|Previous]] | [[GCHP_Basic_Example_Run|Next]] | [[Getting_Started_With_GCHP|User Manual Home]] | [[GEOS-Chem_HP|GCHP Home]]'''''
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'''''[[Downloading_GCHP|Previous]] | [[Obtaining_a_GCHP_Run_Directory|Next]] | [[Getting Started with GCHP]] | [[GCHP Main Page]]'''''

Latest revision as of 15:40, 8 December 2020


The GCHP documentation has moved to https://gchp.readthedocs.io/. The GCHP documentation on http://wiki.seas.harvard.edu/ will stay online for several months, but it is outdated and no longer active!


Previous | Next | Getting Started with GCHP | GCHP Main Page

  1. Hardware and Software Requirements
  2. Setting Up the GCHP Environment
  3. Downloading Source Code and Data Directories
  4. Compiling
  5. Obtaining a Run Directory
  6. Running GCHP: Basics
  7. Running GCHP: Configuration
  8. Output Data
  9. Developing GCHP
  10. Run Configuration Files


Compiling GCHP is the same procedure as compiling GEOS-Chem Classic. Please see Compiling with CMake for instructions.


Previous | Next | Getting Started with GCHP | GCHP Main Page