noresm:settingupcamonlinuxpc

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noresm:settingupcamonlinuxpc [2014-03-05 12:06:35]
alfg [Obtain CAM 5.3 source code] 		noresm:settingupcamonlinuxpc [2022-05-31 09:29:32] (current)
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 **To use the development version of CAM5-Oslo, check out NorESM (not CESM) from the noresm repository** **To use the development version of CAM5-Oslo, check out NorESM (not CESM) from the noresm repository**
 <file> <file>
-svn checkout https://svn.met.no/NorESM/noresm/branches/featureCAM5-OsloDevelopment_trunk2.0-1 myCamOsloDev+svn checkout https://svn.met.no/NorESM/noresm/branches/featureCAM5-OsloDevelopment_trunk2.0-4 myCamOsloDev
 </file> </file>
 ===== Compile the netcdf libraries using gfortran ===== ===== Compile the netcdf libraries using gfortran =====
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   * export CXXFLAGS=-O0   * export CXXFLAGS=-O0
  
-The netcdf c-library complains about a non-successful compilation because it can not find Doxyfile. This is not important.+The netcdf c-library complains about a non-successful compilation because it can not find Doxyfile. This is not important. The compilation needs also the following env-variables: CPPFLAGS=-I${dir}/include, LDFLAGS=-L${dir}/lib, where "dir" is directory you use for the "configure" scripts
  
 3) Get the netcdf source code (including the c-headers) from  3) Get the netcdf source code (including the c-headers) from 
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 c) make install c) make install
  
-4) Get fortran netcdf api (http://www.unidata.ucar.edu/downloads/netcdf/netcdf-fortran/index.jsp) and follow+4) Get fortran netcdf api (http://www.unidata.ucar.edu/downloads/netcdf/index.jsp) and follow
 http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-fortran-install.html http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-fortran-install.html
  
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   * export CSMDATA=/path/to/cam/input/data   * export CSMDATA=/path/to/cam/input/data
  
-This command compiles CAM (not including any CAM-Oslo code) on my machine+This command configures CAM (not including any CAM-Oslo code) on my machine. It creates a Makefile used later for compilation.
  
 <file> <file>
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 </file> </file>
  
-As long as $camcfg is defined, you can execute this from any directory..+**As long as $camcfg is defined, you can execute this from any directory..**
  
-Then you need the following commands+Then you need the following commands **executed from the same directory as you executed "configure"**
 <file> <file>
 $camcfg/build-namelist -test -config config_cache.xml $camcfg/build-namelist -test -config config_cache.xml
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 </file> </file>
  
-===== Including cam-oslo code ===== +Finally run the model simply executing the command
- +
-Some cam-oslo code has been preliminary ported to work in CAM 5.3 to run alongside CESM1.2. This code can be accessed with git using the command:  +
 <file> <file>
-git clone ssh://username@hexagon.bccs.uib.no/work/shared/noresm/repos/cam_oslo.git +./cam
 </file> </file>
-(Execute the command from ~/CESM_1_2_0/cesm1_2_0/models/atm/cam/src/physics/ so that a cam_oslo directory is created there.) 
  
-**The git repository is now deprecated, and users are encouraged to check out the CAM5-OsloDevelopment branch of NorESM**+ 
 +NOTE: In CAM5.5 (upcoming versions) this same procedure is supposed to work with the following command (NOT VERIFIED): 
 <file> <file>
-svn checkout https://svn.met.no/NorESM/noresm/branches/featureCAM5-OsloDevelopment_trunk2.0-1 myCamOsloDev+$camcfg/configure -fc gfortran -fc_type gnu -debug -nospmd -nosmp -dyn fv -res 10x15 -ice sice -phys cam5
 </file> </file>
  
-**In order to include CAM-Oslo code you need to change the config-options:**+===== Including cam-oslo code ===== 
 + 
 +This assumes you checked out NorESM (and CESM) with subversion 
 + 
 +Works with latest version of oslo aerosol development branch
 <file> <file>
- $camcfg/configure -dyn fv -debug -hgrid 10x15 -fc gfortran -nospmd -nosmp -test -fc_type gnu -cam_oslo aerlife -cam_oslo_pc true+ $camcfg/configure -dyn fv -debug -hgrid 10x15 -fc gfortran -nospmd -nosmp -test -fc_type gnu -chem trop_mam_oslo 
 </file> </file>
 +
  
 There are additional input needed for the CAM-Oslo code. They are available in the same input-directory as the normal CESM-input files. There are additional input needed for the CAM-Oslo code. They are available in the same input-directory as the normal CESM-input files.
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 gdb has problems with printing info about allocatable arrays. Allocatable arrays have to be displayed as "*((real_8 *)my_array + N)@M" where N is number of elements beyond first element and M is number of elements to show. (See bottom of this page (and links therein) http://stackoverflow.com/questions/11786958/how-to-print-fortran-arrays-in-gdb)  gdb has problems with printing info about allocatable arrays. Allocatable arrays have to be displayed as "*((real_8 *)my_array + N)@M" where N is number of elements beyond first element and M is number of elements to show. (See bottom of this page (and links therein) http://stackoverflow.com/questions/11786958/how-to-print-fortran-arrays-in-gdb) 
 +
 +It is sometimes useful to let the compiler tell you about additional errors. Assuming you use gfortran on your PC: See https://gcc.gnu.org/onlinedocs/gfortran/Code-Gen-Options.html for additional options. For example if you want to check just about everything, add "-fcheck=all" to the "FC_FLAGS" in the gfortran section. (Note: Running configure again re-generates the Makefile)
  
  
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 Save the xml-file to the use_cases directory as "my_case.xml" and run the command Save the xml-file to the use_cases directory as "my_case.xml" and run the command
  
 +<file>
 $camcfg/build-namelist -test -config config_cache.xml -use_case my_case $camcfg/build-namelist -test -config config_cache.xml -use_case my_case
 +</file>
  
 <file> <file>
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