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Community Climate System Model (CCSM) version 3.0 installation.

We have installed and run the CCSM3 on the IARC computer "chena", that is an SMP computer with 4 dual-core AMD Opteron processors, operated by the Debian Linux (Belchansky et al, 2006). This manual summarizes the discussions in the CCSM3 and PGI user forums and lists the procedures, neccessary to run the CCSM3 on the "chena"-like systems, serving as an addendum to the CCSM3 manuals.

  1. Installing the libraries and utilities, required by the CCSM:
  2. Tuning operating environment to provide proper conditions for the model successful compilation and run.
    • The following environment variables were set pointing to the directories with headers and library files of the installed MPI and NetCDF
      INC_NETCDF
      INC_MPI
      LIB_NETCDF
      LIB_MPI
      These variables aren't mentioned in the CCSM 3.0 documentation, they appear only in the model compilation scripts. The PGI compiler gets the empty -I switch unless they are set, and returns the error "Value required for command line switch: -idir".
    • The system semaphores were increased with adding the following line to the /etc/sysctl.conf
      kernel/sem = 250 32000 100 384
  3. Modification of the model scripts and source code required for the "chena".
    • New machine support scripts were added to the model source code as described in the documentation. The .run script must contain the command limit stacksize unlimited in its beginning, to prevent sigsegv(11) runtime errors.
    • Modifications to the CCSM3 source code.

      CAM, file cam.F90, line 101:
      call shr_msg_stdio('atm')
      was moved AFTER
      call cpl_interface_init(cpl_fields_atmname,mpicom)

      CLM, file program_csm.F90, line 165:
      call shr_msg_stdio ('lnd')
      was moved AFTER calls of MPI setup.
      The changes above make the model to satisfy the requirements of the MPICH documentation recommending doing as less as possible before calls to MPI_INIT, particularly, avoiding opening files and changing the working directories.

  4. The Model Coupling Toolkit (MCT) library, included as a part of the CCSM bundle, was updated from the version 2.0.1 to the version 2.2.0.
  5. The load balancing procedure has resulted in the following configuration: 1 cpl, 2 ocn, 2 lnd, 16 atm, 2 ice. This configuration gives the peak performance of 2.01 model years per wallclock day with the T31_gx3v5 resolution, estimated from the 10-day run.
  6. NCAR Command Language (NCAR) and R (R-project, with ncdf package) were installed on the "chena" for processing the CCSM output.

References

Belchansky, G. I., Eremeev V.A., Kozlenko N.N., Mordvintsev I.N., Platonov N.G., and Alexeev V.A. (2006) Study of uncertainty of sea ice albedo in the Arctic in observations and modeling, IARC final project report.