COLA Benchmark (August, 2004)

Instructions
Codes
Manifest
Known Issues
Updates
Output

Instructions:

Construct a base directory for the run. Within that directory, construct a subdirectory ./Library. Download gemslib.tgz, eq_state.tgz and neptune.tgz into that Library subdirectory. Un-tar then build the three libraries (make neptune last).
Return to the base directory and download supervisor.tgz, restarts.tgz, bcs.tgz and scripts.tgz.
Build the main program from ./supervisor
Download and apply updates and corrections (See Below).

Pseudo-script:

mkdir benchmark cd benchmark BASEDIR=`pwd` mkdir Library cd Library LIBDIR=`pwd` >> get gemslib.tgz eq_state.tgz neptune.tgz << tar xzf gemslib.tgz cd gems/gemslib_mpi_32 make cd $LIBDIR tar xzf eq_state.tgz cd eq_state/wright/lib_red_32 make cd $LIBDIR tar xzf neptune.tgz cd neptune/lib_red_32 make cd $BASEDIR >> get supervisor.tgz << tar xzf supervisor.tgz cd supervisor make cd $BASEDIR >> get restarts.tgz bcs.tgz scripts.tgz << tar xzf restarts.tgz tar xzf bcs.tgz tar xzf scripts.tgz submit ./run

Library Codes:

MPI based GEMS Library (gzipped tar file gemslib.tgz 103K)
Wright Equation of State Library (eq_state.tgz 27K)
Poseidon Model Library (neptune.tgz 280K)

Main Code, Scripts, Data Files for 5/8 x 1/3 global run:

Supervisor Code (supervisor.tgz 20K)
Restart and grid file (restarts.tgz 102M)
Boundary conditions and forcing (bcs.tgz 110M)
Run script and parameter files (scripts.tgz 2K)

Manifest:

Main directory:

     3619  run
      194  clock.namelist
     1563  layer_control
 14874720  bcs/dQ_climatology
 14874816  bcs/LH_climatology
  1239560  bcs/pendepth_climatology
 14874720  bcs/Q0_climatology
 14874816  bcs/rain_data
 14874816  bcs/SW_data
 14874720  bcs/Sobs_climatology
 14874816  bcs/taux_data
 14874816  bcs/tauy_data
 14874720  bcs/Tobs_climatology
  7447096  restarts/gridfile
307414144  restarts/p_12_2004
     6290  supervisor/Makefile
    10072  supervisor/fakearies.f90
     2587  supervisor/faries.f90
    10107  supervisor/faries.read.f90
     3972  supervisor/faries.setup.f90
     6634  supervisor/fbio.f90
    41756  supervisor/super1.f90

Library:27211 gems/gemslib_mpi_32/arrays_module.f90 1009 gems/gemslib_mpi_32/assert.f90 147794 gems/gemslib_mpi_32/communication_primitives.f90 340475 gems/gemslib_mpi_32/communication_utilities.f90 66813 gems/gemslib_mpi_32/coupler.f90 23463 gems/gemslib_mpi_32/DEPENDENT.generic.f90 94751 gems/gemslib_mpi_32/ghost_module.f90 7386 gems/gemslib_mpi_32/grid_types.f90 113181 gems/gemslib_mpi_32/grid_utilities.f90 44660 gems/gemslib_mpi_32/grids_module.f90 5568 gems/gemslib_mpi_32/hermes_types.f90 429 gems/gemslib_mpi_32/kind_module.f90 2405 gems/gemslib_mpi_32/Makefile 4108 gems/gemslib_mpi_32/mpif.f90.in 5465 gems/gemslib_mpi_32/mpif90.h 11296 gems/gemslib_mpi_32/p_linear_algebra.f90 18333 gems/gemslib_mpi_32/polygon.f90 1197 gems/gemslib_mpi_32/README 37060 gems/gemslib_mpi_32/rotate.f90 29761 gems/gemslib_mpi_32/tbd.f90 184605 gems/gemslib_mpi_32/zeus_clocks.f90 3687 eq_state/wright/lib_red_32/eos80.f90 31534 eq_state/wright/lib_red_32/eq_state.f90 1867 eq_state/wright/lib_red_32/global_constants.f90 694 eq_state/wright/lib_red_32/kind_module.f90 1192 eq_state/wright/lib_red_32/Makefile 6100 eq_state/wright/lib_red_32/test_program.f90 74192 eq_state/wright/lib_red_32/test_program.output 8979 neptune/lib_red_32/budget.module.f90 165683 neptune/lib_red_32/diagnostics.module.f90 4705 neptune/lib_red_32/gems.f90 14924 neptune/lib_red_32/gemsX.ibm.mpi.f90 108873 neptune/lib_red_32/gemsX.mpi.f90 2040 neptune/lib_red_32/global_constants.f90 2558 neptune/lib_red_32/ieee.f90 20113 neptune/lib_red_32/kappa.f90 694 neptune/lib_red_32/kind_module.f90 7578 neptune/lib_red_32/Makefile 12724 neptune/lib_red_32/OptionalArray.module.f90 36288 neptune/lib_red_32/poseidon.budget.f90 118667 neptune/lib_red_32/poseidon.f90 113157 neptune/lib_red_32/poseidon.grid.f90 264352 neptune/lib_red_32/poseidon.hydro.f90 36176 neptune/lib_red_32/poseidon.misc.f90 63304 neptune/lib_red_32/poseidon.ohist.f90 128720 neptune/lib_red_32/poseidon.restarts.f90 14096 neptune/lib_red_32/poseidon_physinfo_module.f90 73255 neptune/lib_red_32/poseidon_types.f90 142265 neptune/lib_red_32/remap_module.f90 35475 neptune/lib_red_32/shapiro.f90 81277 neptune/lib_red_32/zdf_module.f90

Known Issues:

mpif.h

The main problem facing the deployment of this benchmark is the linkage to the MPI library, and the use of mpif.h or mpif90.f90 include. This occurs when compiling communications_primitives.f90 in gems/gemslib_mpi_32.

flush()

The flush() subroutine is available with some compiler systems, and not with others. In the supplied code, neptune/lib_red_32/gems.f90, we have included

 
175:  use XLFUTILITY, only: FLUSH_
 
196:  subroutine FLUSH( lunit, errno )
197:  integer, intent(in)  :: lunit
198:  integer, intent(out),optional :: ERRNO
199:  if ( PRESENT(ERRNO) ) errno=0
200:  
201:! If whe have a FLUSH, use it 
202:!  On IBM, flush is flush_ 
203: 
204:	call FLUSH_(lunit)  
205:
206:  end subroutine FLUSH

This code may be removed and/or replaced with appropriate calls. Flush is not necessary in the routine operation of the model. It simply ensures that I/O buffers are flushed. A suitable change is to simply delete line 175 and 204.

Fortran95 - C interaction

A possible problem has been identified with the Poseidon code, in that it passes array sections to GEMS subroutines that then call MPI procedures that are written in C. Contact Paul Schopf for further details, or should any problem arise in execution.

Running the executable:

The sample script uses the prun facility of the HP-Compaq Alphaserver system at NASA GSFC. A suitablle mpirun command is needed.

Updates

An issue regarding the use of conflicting unit numbers was identified after the release of the original benchmark. An update file contains a modified version of the neptune/lib_red_32/zdf_module.f90 neptune/lib_red_32/poseidon.grid.f90 and supervisor/faries.f90 codes. These may be downloaded as a gzipped tar file HERE.

To install the update, replace zdf_module.f90 and poseidon.grid.f90 in the poseidon library and re-make the library. Then put the new faries.f90 code in supervisor and re-make.

CVS tree for cvs_mirror: HERE (2.7M)

Output

The STDOUT produced by the benchmark code running on 32 PEs at NASA GSFC is available here.

Last modified: August 26, 2004 9:15 AM

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