Compile with Make¶
Now that CMake has created the Makefiles that are needed to compile GEOS-Chem, you may proceed as follows:
Build the GEOS-Chem Classic executable¶
Use the make command to build the GEOS-Chem executable. Type:
$ make -j
You will see output similar to this:
Scanning dependencies of target HeadersHco Scanning dependencies of target Isorropia Scanning dependencies of target KPP_FirstPass [ 1%] Building Fortran object src/HEMCO/src/Shared/Headers/CMakeFiles/HeadersHco.dir/hco_inquireMod.F90.o [ 1%] Building Fortran object src/HEMCO/src/Shared/Headers/CMakeFiles/HeadersHco.dir/hco_precision_mod.F90.o [ 1%] Building Fortran object src/HEMCO/src/Shared/Headers/CMakeFiles/HeadersHco.dir/hco_charpak_mod.F90.o [ 3%] Building Fortran object src/GEOS-Chem/KPP/fullchem/CMakeFiles/KPP_FirstPass.dir/gckpp_Monitor.F90.o [ 3%] Building Fortran object src/GEOS-Chem/KPP/fullchem/CMakeFiles/KPP_FirstPass.dir/gckpp_Precision.F90.o [ 3%] Building Fortran object src/GEOS-Chem/KPP/fullchem/CMakeFiles/KPP_FirstPass.dir/gckpp_Parameters.F90.o [ 3%] Linking Fortran static library libKPP_FirstPass.a [ 3%] Built target KPP_FirstPass Scanning dependencies of target Headers [ 3%] Building Fortran object src/GEOS-Chem/ISORROPIA/CMakeFiles/Isorropia.dir/isorropiaII_main_mod.F.o [ 3%] Building Fortran object src/GEOS-Chem/Headers/CMakeFiles/Headers.dir/charpak_mod.F90.o [ 3%] Building Fortran object src/GEOS-Chem/Headers/CMakeFiles/Headers.dir/dictionary_m.F90.o [ 3%] Building Fortran object src/GEOS-Chem/Headers/CMakeFiles/Headers.dir/CMN_SIZE_mod.F90.o [ 3%] Building Fortran object src/GEOS-Chem/Headers/CMakeFiles/Headers.dir/qfyaml_mod.F90.o [ 4%] Building Fortran object src/GEOS-Chem/Headers/CMakeFiles/Headers.dir/CMN_O3_mod.F90.o [ 6%] Building Fortran object src/GEOS-Chem/Headers/CMakeFiles/Headers.dir/inquireMod.F90.o ... etc ... [ 93%] Building Fortran object src/GEOS-Chem/GeosCore/CMakeFiles/GeosCore.dir/sulfate_mod.F90.o [ 93%] Building Fortran object src/GEOS-Chem/GeosCore/CMakeFiles/GeosCore.dir/fullchem_mod.F90.o [ 93%] Building Fortran object src/GEOS-Chem/GeosCore/CMakeFiles/GeosCore.dir/mixing_mod.F90.o [ 93%] Building Fortran object src/GEOS-Chem/GeosCore/CMakeFiles/GeosCore.dir/carbon_mod.F90.o [ 95%] Building Fortran object src/GEOS-Chem/GeosCore/CMakeFiles/GeosCore.dir/chemistry_mod.F90.o [ 95%] Building Fortran object src/GEOS-Chem/GeosCore/CMakeFiles/GeosCore.dir/gc_environment_mod.F90.o [ 96%] Building Fortran object src/GEOS-Chem/GeosCore/CMakeFiles/GeosCore.dir/emissions_mod.F90.o [ 96%] Building Fortran object src/GEOS-Chem/GeosCore/CMakeFiles/GeosCore.dir/cleanup.F90.o [ 98%] Linking Fortran static library libGeosCore.a [ 98%] Built target GeosCore Scanning dependencies of target gcclassic [ 98%] Building Fortran object src/CMakeFiles/gcclassic.dir/GEOS-Chem/Interfaces/GCClassic/main.F90.o [100%] Linking Fortran executable ../bin/gcclassic [100%] Built target gcclassic
The -j argument tells make that it can execute as many jobs as it wants simultaneously. For example, if you have 8 cores, then the build process may attempt to compile 8 files at a time.
If you want to restrict the number of simultaneous jobs (e.g. you are compiling on a machine with limited memory), you can can use e.g. make -j4, which should only try to compile 4 files at a time.
Install the executable in your run directory¶
Now that the
gcclassic executable is built, install it to your
run directory with make install. For this to work properly,
you must tell CMake where to find your run directory by configuring
described above. Type:
$ make install
and you will see output similar to this:
[ 1%] Built target HeadersHco [ 3%] Built target KPP_FirstPass [ 3%] Built target Isorropia [ 4%] Built target JulDayHco [ 13%] Built target Headers [ 18%] Built target NcdfUtilHco [ 19%] Built target JulDay [ 19%] Built target GeosUtilHco [ 25%] Built target NcdfUtil [ 40%] Built target HCO [ 46%] Built target GeosUtil [ 56%] Built target HCOX [ 59%] Built target Transport [ 62%] Built target History [ 63%] Built target ObsPack [ 71%] Built target KPP [ 71%] Built target HCOI_Shared [ 98%] Built target GeosCore [100%] Built target gcclassic Install the project... -- Install configuration: "Release" -- Up-to-date: /home/ubuntu/gc_merra2_fullchem/build_info/CMakeCache.txt -- Up-to-date: /home/ubuntu/gc_merra2_fullchem/build_info/summarize_build -- Up-to-date: /home/ubuntu/gc_merra2_fullchem/gcclassic
Let’s now navigate back to the run directory and get a directory listing:
$ cd .. $ ls CodeDir@ cleanRunDir.sh* GEOSChem.Restart.20190701_0000z.nc4 download_data.py* HEMCO_Config.rc download_data.yml HEMCO_Config.rc.gmao_metfields gcclassic* HEMCO_Diagn.rc geoschem_config.yml HISTORY.rc getRunInfo* OutputDir/ metrics.py* README runScriptSamples@ archiveRun.sh* rundirConfig/ build/ species_database.yml build_info/
You should now see the gcclassic executable and a
directory there. GEOS-Chem has now been configured, compiled, and
installed in your run directory.
Please see the Run directory files and folders section for more information about the contents of the run directory.
You are now ready to run a GEOS-Chem simulation!
Remove compiler-generated files when no longer needed¶
In older versions of GEOS-Chem, you could use a GNU Make command such
as make clean or make realclean to remove all
.o), library (
.a), module (
files, as well as the previously-built executable file from the
GEOS-Chem source code folder.
All of the files created by Cmake during the configuration and
compilation stages are placed in the
build/ folder in your run
directory (or in the location that you have specified with the
-DRUNDIR=/path/to/run/dir option.). Therefore, if you
wish to build the GEOS-Chem Classic executable from
scratch, all you have to do is to remove all of the files from the
build folder. It’s as simple as that!
You can also create a new build folder with this command:
$ mv build was.build $ mkdir build
and then later on, you can remove the old build folder:
$ rm -rf was.build
This avoids the temptation to use rm -rf *, which can potentially wipe out all of your files if used incorrectly.