Problem when building CAM for CESM1.2 with compset F_2000_CAM5_PM (prescribed aerosol)

[chen63@illinois_edu]

I am trying to run the compset F_2000_CAM5_PM for prescribed MAM3 aerosols in CESM1.2 on NERSC Hopper. The resolution I used is f19_f19. When I build the executable, I got the following message:-------------------------------------------------------------------------
CESM BUILDNML SCRIPT STARTING
- To prestage restarts, untar a restart.tar file into /scratch/scratchdirs/chen63/FC5PM_f19_f19/run
infile is /global/homes/c/chen63/runs/FC5PM_f19_f19/Buildconf/cplconf/cesm_namelist
CAM writing dry deposition namelist to drv_flds_in
Writing ocean component namelist to ./docn_in
CAM writing namelist to atm_in
CLM configure done.
CLM adding use_case 2000_control defaults for var sim_year with val 2000
CLM adding use_case 2000_control defaults for var sim_year_range with val constant
CLM adding use_case 2000_control defaults for var use_case_desc with val Conditions to simulate 2000 land-use
CICE configure done.
CESM BUILDNML SCRIPT HAS FINISHED SUCCESSFULLY
-------------------------------------------------------------------------
-------------------------------------------------------------------------
CESM PRESTAGE SCRIPT STARTING
- Case input data directory, DIN_LOC_ROOT, is /project/projectdirs/ccsm1/inputdata
- Checking the existence of input datasets in DIN_LOC_ROOT
Attempting to download missing data:
Input Data List Files Found:
/global/homes/c/chen63/runs/FC5PM_f19_f19/Buildconf/cpl.input_data_list
/global/homes/c/chen63/runs/FC5PM_f19_f19/Buildconf/cam.input_data_list
/global/homes/c/chen63/runs/FC5PM_f19_f19/Buildconf/clm.input_data_list
/global/homes/c/chen63/runs/FC5PM_f19_f19/Buildconf/cice.input_data_list
/global/homes/c/chen63/runs/FC5PM_f19_f19/Buildconf/docn.input_data_list
/global/homes/c/chen63/runs/FC5PM_f19_f19/Buildconf/rtm.input_data_list
export https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/atm/cam/chem/trop_mam/aero/mam3_1.9x2.5_L30_2000clim_c130319.nc /project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero/mam3_1.9x2.5_L30_2000clim_c130319.nc ..... mkdir: cannot create directory `/project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero': Permission denied
svn: E000002: Can't create temporary file from template '/project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero/svn-XXXXXX': No such file or directory
export https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/atm/cam/chem/trop_mam/aero /project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero ..... svn: E000013: Can't make directory '/project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero': Permission denied
export https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/atm/cam/chem/trop_mam/aero/mam3_1.9x2.5_L30_2000clim_c130319.nc /project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero/mam3_1.9x2.5_L30_2000clim_c130319.nc ..... mkdir: cannot create directory `/project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero': Permission denied
svn: E000002: Can't create temporary file from template '/project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero/svn-XXXXXX': No such file or directory
export https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/atm/cam/chem/trop_mam/aero /project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero ..... svn: E000013: Can't make directory '/project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero': Permission denied The following files were not found, they are required
Input Data List Files Found:
/global/homes/c/chen63/runs/FC5PM_f19_f19/Buildconf/cpl.input_data_list
/global/homes/c/chen63/runs/FC5PM_f19_f19/Buildconf/cam.input_data_list
/global/homes/c/chen63/runs/FC5PM_f19_f19/Buildconf/clm.input_data_list
/global/homes/c/chen63/runs/FC5PM_f19_f19/Buildconf/cice.input_data_list
/global/homes/c/chen63/runs/FC5PM_f19_f19/Buildconf/docn.input_data_list
/global/homes/c/chen63/runs/FC5PM_f19_f19/Buildconf/rtm.input_data_list
File is missing: /project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero/mam3_1.9x2.5_L30_2000clim_c130319.nc
File is missing: /project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero
File is missing: /project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero/mam3_1.9x2.5_L30_2000clim_c130319.nc
File is missing: /project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero
Invoke the following command to obtain them
./check_input_data -inputdata /project/projectdirs/ccsm1/inputdata -exportThen, when I run "./check_input_data -inputdata /project/projectdirs/ccsm1/inputdata -export", I got the following message:Input Data List Files Found:
./Buildconf/cpl.input_data_list
./Buildconf/cam.input_data_list
./Buildconf/clm.input_data_list
./Buildconf/cice.input_data_list
./Buildconf/docn.input_data_list
./Buildconf/rtm.input_data_list
export https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/atm/cam/chem/trop_mam/aero/mam3_1.9x2.5_L30_2000clim_c130319.nc /project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero/mam3_1.9x2.5_L30_2000clim_c130319.nc ..... mkdir: cannot create directory `/project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero': Permission denied
svn: Can't open '/project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero/tempfile.tmp': No such file or directory
export https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/atm/cam/chem/trop_mam/aero /project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero ..... svn: Can't make directory '/project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero': Permission denied
export https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/atm/cam/chem/trop_mam/aero/mam3_1.9x2.5_L30_2000clim_c130319.nc /project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero/mam3_1.9x2.5_L30_2000clim_c130319.nc ..... mkdir: cannot create directory `/project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero': Permission denied
svn: Can't open '/project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero/tempfile.tmp': No such file or directory
export https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/atm/cam/chem/trop_mam/aero /project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero ..... svn: Can't make directory '/project/projectdirs/ccsm1/inputdata/atm/cam/chem/trop_mam/aero': Permission deniedCould someone please help me with this? Thanks a lot!Yanju

 

[jedwards]

The data needs to be staged by a member of the cseg group.   I have started the process, will let you know when it is complete.

 

[rambhari0123@gmail_com]

Yanju, What i feel is that the script "./check_input_data -inputdata /project/projectdirs/ccsm1/inputdata -export" is trying to locate the inputdata in CESM data repository, i found the data files, next it tries copy the data repository structure and data file in your inputdata tree. but svn working on your machine was unable to do due the permission given to your account. So, i suggest you contact the machine admins to look into permission issue OR You can do the same work by downloading the required files manually and transfer at required path and data tree. It definitly  would works.Cheers !!Ram 

 

[jedwards]

There was a filesystem problem on hopper shortly after my first reply and the data transfer was delayed - it's complete now and you should be able to go ahead with your run.

 

[chen63@illinois_edu]

Hi, Edwards,Thanks a lot for your help and yes now I am able to run the compset. Could you please help me with the following questions?(1) Can we only prescribe a certain type of the aerosols (for example, dust) with CESM1.2?(2) I looked at the input data file for prescribed aerosols. There are variables as XX_a1_logm and XX_a1_logv, do they mean the log10 of the mixing ratio? As the units are both kg/kg, I don't know what m and v means in this case (previously I though they could stand for mass and volume).Thank you!Yanju

 

[eaton]

1) The purpose of the rad_climate namelist variable is to specify which species will influence the climate.  By default if prognostic MAM is running then the prognostic aerosols will affect the climate (note that this is completely specified by the rad_climate variable).  If MAM is not active when running with cam5 physics, then it is assumed that prescribed modal aerosol species are present and these are specified in the rad_climate variable.  Any modification to these default assumptions would be done by customizing the default value of rad_climate produced by build-namelist.2) The prescribed modal aerosol implementation is not using mixing ratio values that have been time interpolated from monthly mean values as is done for the prescribed bulk aerosols.  Instead the mixing ratio values are obtained by random sampling of the time interpolated log normal distribution of each prescribed specie.  The XX_a1_logm and XX_a1_logv variables are log mean and log of variance values that are used to construct the log normal distribution.