4. Sample Interactive Session

The following sections present an interactive C shell session to build and run a default version of CAM. Most often these steps will be encapsulated in shell scripts. An important advantage of using a script is that it acts to document the run you’ve done. Knowing the source code tree, and the configure and build-namelist commands provides all the information needed to replicate a run.

For the interactive session the shell variable camcfg is set to the directory in the source tree that contains the CAM configure and build-namelist utilities ($CAM_ROOT/models/atm/cam/bld).

Much of the example code in this document is set off in sections like this.
Many examples refer to files in the distribution source tree using
filepaths that are relative to distribution root directory, which we
denote, using a UNIX shell syntax, by $CAM_ROOT.  The notation indicates
that CAM_ROOT is a shell variable that contains the filepath.  This could
just as accurately be referred to as $CCSMROOT since the root directory of
the CESM distribution is the same as the root of the CAM distribution
which is contained within it.

4.1. Configuring CAM for serial execution

We start by changing into the directory in which the CAM executable will be built, and then setting the environment variables INC_NETCDF and LIB_NETCDF which specify the locations of the NetCDF include files and library. This information is required by configure in order for it to produce the Makefile. The NetCDF library is require by all CAM builds. The directories given are just examples; the locations of the NetCDF include files and library are system dependent. The information provided by these environment variables could alternatively be provided via the commandline arguments -nc_inc and -nc_lib.

NOTE: A common problem is to encounter build failures due to specifying a NetCDF library which was built with a different Fortran compiler than the one used to build CAM. Consult your system’s documentation (or some other knowledgeable source) to find the location of the NetCDF library which was built with the Fortran compiler you intend to use.

% cd /work/user/cam_test/bld
% setenv INC_NETCDF /usr/local/include
% setenv LIB_NETCDF /usr/local/lib

Next we issue the configure command (see the example just below). The argument -dyn fv specifies using the FV dynamical core which is the default for CAM5, but we recommend always adding the dynamical core (dycore for short) argument to configure commands for clarity. The argument -hgrid 10x15 specifies the horizontal grid. This is the coarsest grid available for the FV dycore in CAM and is often useful for testing purposes.

We recommend using the -test option the first time CAM is built on any machine. This will check that the environment is properly set up so that the Fortran compiler works and can successfully link to the NetCDF and MPI (if SPMD is enabled) libraries. Furthermore, if the configuration is for serial execution, then the tests will include both build and run phases which may be useful in exposing run time problems that don’t show up during the build, for example when shared libraries are linked dynamically. If any tests fail then it is useful to rerun the configure command and add the -v option which will produce verbose output of all aspects of the configuration process including the tests. If the configuration is for an SPMD build, then no attempt to run the tests will be made. Typically MPI runs must be submitted to a batch queue and are not enabled from interactive sessions. Also the method of launching an MPI job is system dependent. But the build and static linking will still be tested.

% $camcfg/configure -dyn fv -hgrid 10x15 -nospmd -nosmp -test
Issuing command to the CICE configure utility:
   $CAM_ROOT/models/ice/cice/bld/configure -hgrid 10x15 -cice_mode prescribed \
        -ntr_aero 0 -nx 24 -ny 19 -bsizex 6 -bsizey 19 -maxblocks 4 -decomptype blkrobin \
        -cache config_cache_cice.xml -cachedir /work/user/cam_test/bld
CICE configure done.
MCT configure is done.
creating /work/user/cam_test/bld/Filepath
creating /work/user/cam_test/bld/Makefile
creating /work/user/cam_test/bld/config.h
creating /work/user/cam_test/bld/config_cache.xml
Looking for a valid GNU make... using gmake
Testing for Fortran 90 compatible compiler... using pgf95
Test linking to NetCDF library... ok
CAM configure done.

The first line of output from the configure command is an echo of the system command that CAM’s configure issues to invoke the CICE configure utility. CICE’s configure is responsible for setting the values of the CPP macros that are needed to build the CICE code.

After the CICE configure is complete the MCT configure script is executed to create the Makefile for building MCT as a separate library. There is a status line output to indicate success of that process.

The next four lines of output inform the user of the files being created by configure. All these files except for the cache file are required to be in the CAM build directory, so it is generally easiest to be in that directory when configure is invoked.

The output from the -test option tells us that gmake is a GNU Make on this machine; that the Fortran compiler is pgf95; and that code compiled with the Fortran compiler can be successfully linked to the NetCDF library. The CAM configure script is the place where the default compilers are specified. On Linux systems the default is pgf95. Finally, since this is a serial configuration no test for linking to the MPI library was done.

4.2. Specifying the Fortran compiler

In the previous section the configure command was issued without specifying which Fortran compiler to use. For that to work we were depending on the CAM configure script to select a default compiler. One of the differences between the CAM standalone build and a build using the CESM scripts is that CAM’s configure provides defaults based on the operating system name (as determined by the Perl internal variable $OSNAME), while the CESM scripts require the user to specify a specific machine (and compiler if the machine supports more than one) as an argument to the create_newcase command.

The CAM makefile currently recognizes the following operating systems and compilers.

AIX
xlf95_r, mpxlf95_r

Linux
pgf95 (this is the default)

lf95

ifort

gfortran (has had minimal testing)

pathf90 (has had minimal testing)

Darwin
xlf95_r, mpxlf95_r, ifort

BGL
blrts_xlf95

BGP
mpixlf95_r

The above list contains two IBM Blue Gene machines; BGL and BGP. The executables on these machines are produced by cross compilation and hence the configure script is not able to determine the machine for which the build is intented. In this case the user must supply this information to configure by using the -target_os option with the values of either bgl or bgp.

On a Linux platform several compilers are recognized with the default being pgf95. It is assumed that the compiler to be used is in the user’s path (i.e., in one of the directories in the PATH environment variable). If it isn’t then the -test option will issue an error indicating that the compiler was not found.

Suppose for example that one would like to use the Intel compiler on a local Linux system. The CAM makefile recognizes ifort as the name of the Intel compiler. To invoke this compiler use the -fc argument to configure. The following example illustrates the output you get when the compiler you ask for isn’t in your PATH:

% $camcfg/configure -fc ifort -dyn fv -hgrid 10x15 -nospmd -nosmp -test
Issuing command to the CICE configure utility:
$CAM_ROOT/models/ice/cice/bld/configure -hgrid 10x15 -cice_mode prescribed \
-ntr_aero 0 -ntasks 1 -nthreads 1 -cache config_cache_cice.xml \
-cachedir /work/user/cam_test/bld
CICE configure done.
FAILURE: MCT configure

In previous CAM versions this problem would be caught by the -test option, but with the addition of MCT’s configure the problem is now detected there. By default MCT will be build in a subdirectory of the build directory named mct. That directory will contain a file, config.log, which should be examined to track down the cause of the failure. In this case the file contains the message:

$CAM_ROOT/models/utils/mct/configure: line 3558: ifort: command not found

This means that the PATH environment variable has not been correctly set. The first thing to try is to verify the directory that contains the compiler, and then to prepend this directory name to the PATH environment variable.

NOTE: We have made progress porting CAM to the gfortran compiler, but it is still not regularly tested or used for production work.

4.3. Dealing with compiler wrappers

Another instance where the user needs to supply information about the Fortran compiler type to configure is when the compiler is being invoked by a wrapper script. A common example of this is using the mpif90 command to invoke the Fortran compiler that was used to build the MPI libraries. This facilitates correct compilation and linking with the MPI libraries without the user needing to add the required include and library directories, or library names. The same benefit is provided by the ftn wrapper used on Cray XT and XE systems. In the usual case that a Linux OS is being used, since the CAM makefile will not recognize these compiler names, it will assume that the default compiler is being used, and thus will supply compiler arguments that are appropriate for pgf90. The compilation will fail if pgf90 is not the compiler being invoked by the wrapper script (invoking configure with the -test option is a good way to catch this problem). The way to specify which Fortran compiler is being invoked by a wrapper script is via the -fc_type argument to configure. This argument takes one of the values pgi, lahey, intel, pathscale, gnu, or xlf.

CAM’s configure script attempts to determine the compiler type when a compiler specific name is used. It does so by a regular expression match against the unique part of specific compiler names (e.g., any compiler name matching ‘pgf’ will be given the default type of pgi). If the default is wrong then the user will need to manually override the default via setting the -fc_type argument.

4.4. Configuring CAM for parallel execution

Before moving on to building CAM we address configuring the executable for parallel execution. But before talking about configuration specifics let’s briefly discuss the parallel execution capabilities of CAM.

CAM makes use of both distributed memory parallelism implemented using MPI (referred to throughout this document as SPMD), and shared memory parallelism implemented using OpenMP (referred to as SMP). Each of these parallel modes may be used independently of the other, or they may be used at the same time which we refer to as “hybrid mode”. When talking about the SPMD mode we usually refer to the MPI processes as “tasks”, and when talking about the SMP mode we usually refer to the OpenMP processes as “threads”. A feature of CAM which is very helpful in code development work is that the simulation results are independent of the number of tasks and threads used.

Now consider configuring CAM to run in pure SPMD mode. Prior to the introduction of CICE as the sea ice model SPMD was turned on using the -spmd option. But if we try that now we find the following:

% $camcfg/configure -dyn fv -hgrid 10x15 -spmd -nosmp
**    ERROR: If CICE decomposition parameters are not specified, then
**    -ntasks must be specified to determine a default decomposition
**    for a pure MPI run.  The setting was:  ntasks=

A requirement of the CICE model is that its grid decomposition (which is independent of CAM’s decomposition even when the two models are using the same horizontal grid) must be specified at build time. In order for CICE’s configure to set the decomposition it needs to know how much parallelism is going to be used. This information is provided by specifying the number of MPI tasks that the job will use via setting the -ntasks argument.

NOTE: The default CICE decomposition can be overridden by setting

it explicitly using the configure options provided for that purpose.

When running CAM in SPMD mode the build procedure must be able to find the MPI include files and library. The recommended method for doing this is to use scripts provided by the MPI installation to invoke the compiler and linker. On Linux systems a common name for this script is mpif90. The CAM Makefile does not currently use this script by default on Linux platforms, so the user must explicitly specify it on the configure commandline using the -fc argument:

% $camcfg/configure -fc mpif90 -fc_type pgi -cc mpicc -dyn fv -hgrid 10x15 -ntasks 6 -nosmp -test
Issuing command to the CICE configure utility:
$CAM_ROOT/models/ice/cice/bld/configure -hgrid 10x15 -cice_mode prescribed \
-ntr_aero 0 -ntasks 6 -nthreads 1 -cache config_cache_cice.xml \
-cachedir /work/user/cam_test/bld
CICE configure done.
MCT configure is done.
creating /work/user/cam_test/bld/Filepath
creating /work/user/cam_test/bld/Makefile
creating /work/user/cam_test/bld/config.h
creating /work/user/cam_test/bld/config_cache.xml
Looking for a valid GNU make... using gmake
Testing for Fortran 90 compatible compiler... using mpif90
Test linking to NetCDF library... ok
Test linking to MPI library... ok
CAM configure done.

Notice that the number of tasks specified to CAM’s configure is passed through to the commandline that invokes the CICE configure. Generally any number of tasks that is appropriate for CAM to use for a particular horizontal grid will also work for CICE. But it is possible to get an error from CICE at this point in which case either the number of tasks requested should be adjusted, or the options that set the CICE decomposition explicitly will need to be used.

NOTE: The use of the -ntasks argument to configure implies

building for SPMD. This means that an MPI library will be required. Hence, the specification -ntasks 1 is not the same as building for serial execution which is done via the -nospmd option and does not require a full MPI library. (Implementation detail: when building for serial mode a special serial MPI library is used which basically provides a complete MPI API, but doesn’t do any message passing.)

Next consider configuring CAM to run in pure SMP mode. Similarly to SPMD mode, prior to the introduction of the sea ice component CICE the SMP mode was turned on using the -smp option. But with CAM5 that will result in the same error from CICE that we obtained above from attempting to use -spmd. If we are going to run the CICE code in parallel, we need to specify up front how much parallelism will be used so that the CICE configure utility can set the CPP macros that determine the grid decomposition. We specify the amount of SMP parallelism by setting the -nthreads option as follows:

 % $camcfg/configure -dyn fv -hgrid 10x15 -nospmd -nthreads 6 -test
 Issuing command to the CICE configure utility:
 $CAM_ROOT/models/ice/cice/bld/configure -hgrid 10x15 -cice_mode prescribed \
 -ntr_aero 0 -ntasks 1 -nthreads 6 -cache config_cache_cice.xml \
-cachedir /work/user/cam_test/bld
 CICE configure done.
 ...

We see that the number of threads has been passed through to the CICE configure command.

NOTE: The use of the -nthreads argument to configure implies

building for SMP. This means that the OpenMP directives will be compiled. Hence, the specification -nthreads 1 is not the same as building for serial execution which is done via the -nosmp option and does not require a compiler that supports OpenMP.

Finally, to configure CAM for hybrid mode, simply specify both the -ntasks and -nthreads arguments to configure.

4.5. Building CAM

Once configure is successful, build CAM by issuing the make command:

% gmake -j2  >&! make.out

The argument -j2 is given to allow a parallel build using 2 processes. The optimal number of processes to use depends on the compute resource available. There is a lot of available parallelism in the build procedure, so using 16 or even 32 processes may speed things up considerably. Note however that the build happens in shared (not distributed) memory. So specifying more processes than there are processors in a shared memory node is generally not helpful (although the presence of hyperthreading or SMT on a node may provide an advantage to specifying twice the number of processors).

It is useful to redirect the output from make to a file for later reference. This file contains the exact commands that were issued to compile each file and the final command which links everything into an executable file. Relevant information from this file should be included when posting a bug report concerning a build failure.

4.6. Building the Namelist

The first step in the run procedure is to generate the namelist files. The safest way to generate consistent namelist settings is via the build-namelist utility. Even in the case where only a slight modification to the namelist is desired, the best practice is to provide the modified value as an argument to build-namelist and allow it to actually generate the namelist files.

NOTE: The default configuration of CAM using the cam5 physics

package requires that about 60 datasets and dozens of parameter values be specified in order to run correctly. Trying to manage namelists of that complexity by hand editing files is extremely error prone and is strongly discouraged. User modifications to the default namelist settings can be made in a number of ways while still letting build-namelist actually generate the final namelist. In particular, the -namelist, -infile, and -use_case arguments to build-namelist are all mechanisms by which the user can override default values or specify additional namelist variables and still allow build-namelist to do the error and consistency checking which makes the namelist creation process more robust.

The following interactive C shell session builds a default namelist for CAM. We assume that a successful execution of configure was performed in the build directory as discussed in the previous sections. This is an essential prerequisite because the config_cache.xml file produced by configure is a required input file to build-namelist. One of the responsibilities of build-namelist is to set appropriate default values for many namelist variables, and it can only do this if it knows how the CAM executable was configured. That information is present in the cache file. As in the previous section the shell variable camcfg is set to the CAM configuration directory ($CAM_ROOT/models/atm/cam/bld).

We begin by changing into the directory where CAM will be run. It is usually convenient to have the run directory be separate from the build directory. Possibly a number of different runs will be done that each need to have a separate run directory for the output files, but will all use the same executable file from a common build directory. It is, of course, possible to execute build-namelist in the build directory since that’s where the cache file is and so you don’t need to specify to build-namelist where to find that file (it looks in the current working directory by default). But then, assuming you plan to run CAM in a different directory, all the files produced by build-namelist need to be copied to the run directly. If you’re running configure and build-namelist from a script, then you need to know how to specify the filenames for the files that need to be copied. For this reason it’s more robust to change to the run directory and execute build-namelist there. That way if there’s a change to the files that are produced, your script doesn’t break due to the files not all getting copied to the run directory.

Next we set the CSMDATA environment variable to point to the root directory of the tree containing the input data files. Note that this is a required input for build-namelist (this information may alternatively be provided using the -csmdata argument). If not provided then build-namelist will fail with an informative message. The information is required because many of the namelist variables have values that are absolute filepaths. These filepaths are resolved by build-namelist by prepending the CSMDATA root to the relative filepaths that are stored in the default values database.

The build-namelist commandline contains the -config argument which is used to point to the cache file which was produced in the build directory. It also contains the -test argument, explained further below.

% cd /work/user/cam_test
% setenv CSMDATA /fs/cgd/csm/inputdata
% $camcfg/build-namelist -test -config /work/user/cam_test/bld/config_cache.xml
Writing CICE namelist to ./ice_in
Writing RTM namelist to ./rof_in
Writing DOCN namelist to ./docn_ocn_in
Writing DOCN stream file to ./docn.stream.txt
Writing CLM namelist to ./lnd_in
Writing driver namelist to ./drv_in
CAM writing dry deposition namelist to drv_flds_in
Writing ocean component namelist to ./docn_in
CAM writing namelist to atm_in
Checking whether input datasets exist locally...
OK -- found depvel_file = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart/dvel/depvel_monthly.nc
OK -- found tracer_cnst_filelist = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/oxid/oxid_1.9x2.5_L26_clim_list.c090805.txt
OK -- found tracer_cnst_datapath = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/oxid
OK -- found depvel_lnd_file = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart/dvel/regrid_vegetation.nc
OK -- found xs_long_file = /fs/cgd/csm/inputdata/atm/waccm/phot/temp_prs_GT200nm_jpl06_c080930.nc
OK -- found rsf_file = /fs/cgd/csm/inputdata/atm/waccm/phot/RSF_GT200nm_v3.0_c080416.nc
OK -- found clim_soilw_file = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart/dvel/clim_soilw.nc
OK -- found exo_coldens_file = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart/phot/exo_coldens.nc
OK -- found tracer_cnst_file = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/oxid/oxid_1.9x2.5_L26_1850-2005_c091123.nc
OK -- found season_wes_file = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart/dvel/season_wes.nc
OK -- found solar_data_file = /fs/cgd/csm/inputdata/atm/cam/solar/solar_ave_sc19-sc23.c090810.nc
OK -- found soil_erod = /fs/cgd/csm/inputdata/atm/cam/dst/dst_10x15_c090203.nc
OK -- found bndtvs = /fs/cgd/csm/inputdata/atm/cam/sst/sst_HadOIBl_bc_10x15_clim_c050526.nc
OK -- found focndomain = /fs/cgd/csm/inputdata/atm/cam/ocnfrac/domain.camocn.10x15_USGS_070807.nc
OK -- found tropopause_climo_file = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart/ub/clim_p_trop.nc
OK -- found fpftcon = /fs/cgd/csm/inputdata/lnd/clm2/pftdata/pft-physiology.c110425.nc
OK -- found fsnowaging = /fs/cgd/csm/inputdata/lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc
OK -- found fatmlndfrc = /fs/cgd/csm/inputdata/share/domains/domain.lnd.fv10x15_USGS.110713.nc
OK -- found fsnowoptics = /fs/cgd/csm/inputdata/lnd/clm2/snicardata/snicar_optics_5bnd_c090915.nc
OK -- found fsurdat = /fs/cgd/csm/inputdata/lnd/clm2/surfdata/surfdata_10x15_simyr2000_c090928.nc
OK -- found prescribed_ozone_datapath = /fs/cgd/csm/inputdata/atm/cam/ozone
OK -- found prescribed_ozone_file = /fs/cgd/csm/inputdata/atm/cam/ozone/ozone_1.9x2.5_L26_2000clim_c091112.nc
OK -- found liqopticsfile = /fs/cgd/csm/inputdata/atm/cam/physprops/F_nwvl200_mu20_lam50_res64_t298_c080428.nc
OK -- found iceopticsfile = /fs/cgd/csm/inputdata/atm/cam/physprops/iceoptics_c080917.nc
OK -- found water_refindex_file = /fs/cgd/csm/inputdata/atm/cam/physprops/water_refindex_rrtmg_c080910.nc
OK -- found ncdata = /fs/cgd/csm/inputdata/atm/cam/inic/fv/cami_0000-01-01_10x15_L30_c081013.nc
OK -- found bnd_topo = /fs/cgd/csm/inputdata/atm/cam/topo/USGS-gtopo30_10x15_remap_c050520.nc
OK -- found ext_frc_specifier for SO2 = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_so2_elev_2000_c090726.nc
OK -- found ext_frc_specifier for bc_a1 = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_bc_elev_2000_c090726.nc
OK -- found ext_frc_specifier for num_a1 = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_num_a1_elev_2000_c090726.nc
OK -- found ext_frc_specifier for num_a2 = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_num_a2_elev_2000_c090726.nc
OK -- found ext_frc_specifier for pom_a1 = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_oc_elev_2000_c090726.nc
OK -- found ext_frc_specifier for so4_a1 = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_so4_a1_elev_2000_c090726.nc
OK -- found ext_frc_specifier for so4_a2 = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_so4_a2_elev_2000_c090726.nc
OK -- found srf_emis_specifier for DMS = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/aerocom_mam3_dms_surf_2000_c090129.nc
OK -- found srf_emis_specifier for SO2 = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_so2_surf_2000_c090726.nc
OK -- found srf_emis_specifier for SOAG = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_soag_1.5_surf_2000_c100217.nc
OK -- found srf_emis_specifier for bc_a1 = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_bc_surf_2000_c090726.nc
OK -- found srf_emis_specifier for num_a1 = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_num_a1_surf_2000_c090726.nc
OK -- found srf_emis_specifier for num_a2 = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_num_a2_surf_2000_c090726.nc
OK -- found srf_emis_specifier for pom_a1 = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_oc_surf_2000_c090726.nc
OK -- found srf_emis_specifier for so4_a1 = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_so4_a1_surf_2000_c090726.nc
OK -- found srf_emis_specifier for so4_a2 = /fs/cgd/csm/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_so4_a2_surf_2000_c090726.nc
OK -- found mode_defs for so4_a1 = /fs/cgd/csm/inputdata/atm/cam/physprops/sulfate_rrtmg_c080918.nc
OK -- found mode_defs for pom_a1 = /fs/cgd/csm/inputdata/atm/cam/physprops/ocpho_rrtmg_c101112.nc
OK -- found mode_defs for soa_a1 = /fs/cgd/csm/inputdata/atm/cam/physprops/ocphi_rrtmg_c100508.nc
OK -- found mode_defs for bc_a1 = /fs/cgd/csm/inputdata/atm/cam/physprops/bcpho_rrtmg_c100508.nc
OK -- found mode_defs for dst_a1 = /fs/cgd/csm/inputdata/atm/cam/physprops/dust4_rrtmg_c090521.nc
OK -- found mode_defs for ncl_a1 = /fs/cgd/csm/inputdata/atm/cam/physprops/ssam_rrtmg_c100508.nc
OK -- found mode_defs for so4_a2 = /fs/cgd/csm/inputdata/atm/cam/physprops/sulfate_rrtmg_c080918.nc
OK -- found mode_defs for soa_a2 = /fs/cgd/csm/inputdata/atm/cam/physprops/ocphi_rrtmg_c100508.nc
OK -- found mode_defs for ncl_a2 = /fs/cgd/csm/inputdata/atm/cam/physprops/ssam_rrtmg_c100508.nc
OK -- found mode_defs for dst_a3 = /fs/cgd/csm/inputdata/atm/cam/physprops/dust4_rrtmg_c090521.nc
OK -- found mode_defs for ncl_a3 = /fs/cgd/csm/inputdata/atm/cam/physprops/ssam_rrtmg_c100508.nc
OK -- found mode_defs for so4_a3 = /fs/cgd/csm/inputdata/atm/cam/physprops/sulfate_rrtmg_c080918.nc
OK -- found rad_climate for mam3_mode1 = /fs/cgd/csm/inputdata/atm/cam/physprops/mam3_mode1_rrtmg_c110318.nc
OK -- found rad_climate for mam3_mode2 = /fs/cgd/csm/inputdata/atm/cam/physprops/mam3_mode2_rrtmg_c110318.nc
OK -- found rad_climate for mam3_mode3 = /fs/cgd/csm/inputdata/atm/cam/physprops/mam3_mode3_rrtmg_c110318.nc

The first nine lines of output from build-namelist inform the user about the files that have been created. There are namelist files for the ice component (ice_in), the river runoff component (rof_in), the land component (lnd_in), the data ocean component (docn_in, docn_ocn_in), the atmosphere component (atm_in), the driver (drv_in), and a file that is read by both the atmosphere and land components (drv_flds_in). There is also a “stream file” (docn.stream.txt) which is read by the data ocean component. Note that these filenames are hardcoded in the components and cannot be changed without source code modifications.

The next section of output is the result of using the -test argument to build-namelist. As with configure we recommend using this argument whenever a model configuration is being run for the first time. It checks that each of the files that are present in the generated namelists can be found in the input data tree whose root is given by the CSMDATA environment variable. If a file is not found then the user will need to take steps to make that file accessible to the executing model before a successful run will be possible. The following is a list of possible actions:

• Acquire the missing file. If this is a default file supplied by the CESM project then you will be able to download the file from the project’s svn data repository (see Section 2.1.7, “Acquiring Input Datasets”).
• If you have write permissions in the directory under $CSMDATA then add the missing file to the appropriate location there. If you don’t have write permissions under $CSMDATA then put the file in a place where you can (for example, your run directory) and rerun build-namelist with an explicit setting for the file using your specific filepath.

4.6.1. Example: Use build-namelist to specify a dataset in a non-default location.

Suppose that the -test option informed you that the ncdata file cami_0000-01-01_10x15_L30_c081013.nc was not found. You acquire the file from the data repository, but don’t have permissions to write in the $CSMDATA tree. So you put the file in your run directory and issue a build-namelist command that looks like this:

% $camcfg/build-namelist -config /work/user/cam_test/bld/config_cache.xml \
-namelist "&atm ncdata='/work/user/cam_test/cami_0000-01-01_10x15_L30_c081013.nc' /"

Now the namelist in atm_in will contain an initial file (specified by namelist variable ncdata) which will be found by the executing CAM model.

4.7. Acquiring Input Datasets

If you are doing a standard production run that is supported in the CESM scripts, then using those scripts will automatically invoke a utility to acquire needed input datasets. The information in this section is to aid developers using CAM standalone scripts.

The input datasets required to run CAM are available from a Subversion repository located here: https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/. The user name and password for the input data repository will be the same as for the code repository (which are provided to users when they register to acquire access to the CESM source code repository).

4.7.1. Acquire missing dataset

If you have a list of files that you need to acquire before running CAM, then you can either just issue commands interactively, or if your list is rather long then you may want to put the commands into a shell script. For example, suppose after running build-namelist with the -test option you find that you need to acquire the file /fs/cgd/csm/inputdata/atm/cam/inic/fv/cami_0000-01-01_10x15_L26_c030918.nc. And let’s assume that /fs/cgd/csm/inputdata/ is the root directory of the inputdata tree, and that you have permissions to write there. If the subdirectory atm/cam/inic/fv/ doesn’t already exist, then create it. Finally, issue the following commands at an interactive C shell prompt:

% set svnrepo='https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata'
% cd /fs/cgd/csm/inputdata/atm/cam/inic/fv
% svn export $svnrepo/atm/cam/inic/fv/cami_0000-01-01_10x15_L26_c030918.nc
Error validating server certificate for 'https://svn-ccsm-inputdata.cgd.ucar.edu:443':
- The certificate is not issued by a trusted authority. Use the
fingerprint to validate the certificate manually!
- The certificate hostname does not match.
- The certificate has expired.
  Certificate information:
 - Hostname: localhost.localdomain
 - Valid: from Feb 20 23:32:25 2008 GMT until Feb 19 23:32:25 2009 GMT
 - Issuer: SomeOrganizationalUnit, SomeOrganization, SomeCity, SomeState, --
 - Fingerprint: 86:01:bb:a4:4a:e8:4d:8b:e1:f1:01:dc:60:b9:96:22:67:a4:49:ff
  (R)eject, accept (t)emporarily or accept (p)ermanently? p
   A    cami_0000-01-01_10x15_L26_c030918.nc
   Export complete.

The messages about validating the server certificate will only occur for the first file that you export if you answer “p” to the question as in the example above.

4.8. Running CAM

Once the namelist files have successfully been produced, and the necessary input datasets are available, the model is ready to run. Usually CAM will be run with SPMD parallelization enabled, and this requires setting up MPI resources and possibly dealing with batch queues. These issues will be addressed briefly in Section 2.2, “Sample Run Scripts”. But for a simple test in serial mode executed from an interactive shell, we only need to issue the following command:

% /work/user/cam_test/bld/cam >&! cam.log

The commandline above redirects STDOUT and STDERR to the file cam.log. The CAM logfile contains a substantial amount of information from all components that can be used to verify that the model is running as expected. Things like namelist variable settings, input datasets used, and output datasets created are all echoed to the log file. This is the first place to look for problems when a model run is unsuccessful. It is also very useful to include relevant information from the logfile when submitting bug reports.