lpj.1



     NAME
          lpj, lpjml - Dynamic global vegetation model with managed
          land use and river routing

     SYNOPSIS
          lpjml [-h] [-v] [-vv] [-fpe] [-output {gather|mpi2|buffer}]
          [-outpath dir] [-inpath dir] [-restartpath dir]
          [[-Dmacro[=value]] [-Idir] ...] [filename]

          lpj [-h] [-v] [-vv] [-fpe] [-output {gather|mpi2|buffer}]
          [-outpath dir] [-inpath dir] [-restartpath dir]
          [[-Dmacro[=value]] [-Idir] ...] [filename]

     DESCRIPTION
          The model simulates vegetation dynamics, hydrology and soil
          organic matter dynamics on an area-averaged grid cell basis
          using one-year time step. The name derives from the three
          locations Lund-Potsdam-Jena but is no longer to be
          interpreted that way. Input parameters are monthly mean air
          temperature, total precipitation and percentage of full
          sunshine, annual atmospheric CO2 concentration and soil
          texture class. The simulation for each grid cell begins from
          "bare ground", requiring a "spin up" (under non-transient
          climate) of c. 1000 years to develop equilibrium vegetation
          and soil structure. A restart file can be created to save
          compute time for the spin-up phase.

     OPTIONS
          -h   display a short help text

          -v   print information about program version, operating
               system, compiler used, and compiler flags set.

          -vv  verbosely print the actual values during reading of the
               configuration files.

          -fpe enable floating point exceptions. A core file is
               generated in case of an arithmetic error. Option is
               only available if lpjml has been compiled with
               -DWITH_FPE flag.

          -output {gather|mpi2|buffer}
               use the given output method to write data to disk.
               Valid output methods are gather, mpi2, and buffer. The
               default output method is gather sending all output to
               the root task. If memory allocation fails use other
               output method. Method mpi2 uses MPI-2 parallel file
               functions, while method buffer stores all output in
               memory.  If memory allocation fails for buffer use
               other output method. The option is only valid for the
               MPI version of the code.

          -outpath dir
               set the output directory path. The path is added to the
               output filenames if they do not contain an absolute
               path.

          -inpath dir
               set the input directory path. The path is added to the
               input filenames if they do not contain an absolute
               path.

          -restartpath dir
               set the restart directory path. The path is added to
               the restart filenames if they do not contain an
               absolute path.

          -Dmacro[=value]
               define macro for the preprocessor of the configuration
               file

          -Idir
               define include directory for the preprocessor of the
               configuration file

          filename
               name of configuration file, default is lpjml.conf for
               lpjml and lpj.conf for lpj.

     EXAMPLES
          Perform simulation with input from the /scratch file system:
               lpjml -inpath /scratch/02/lpj

     enabled:
          Start simulation from restart file with floating point exceptions
               lpjml -DFROM_RESTART -fpe lpjml.conf

          For running the MPI version of the program on more than one
          task the lpjsubmit script has to be used.

     ENVIRONMENT
          LPJCONFIG
               default LPJmL configuration filename

          LPJPREP
               defines preprocessor command for LPJmL configuration
               file, default is cpp -P.

          LPJROOT
               defines the root directory for LPJmL. This directory is
               added to the include directories of the preprocessor.
               Invoking lpj_paths.sh or lpj_paths.csh will set this
               environment variable correctly.

          LPJINPATH
               path appended to the input filenames. Only done for
               filenames without absolute path. Same as '-inpath dir'
               option.

          LPJOPTIONS
               runtime options for the preprocessor of LPJmL
               configuration files

          LPJOUTPATH
               path appended to the output filenames. Only done for
               filenames without absolute path. Same as '-outpath dir'
               option.

          LPJRESTARTPATH
               path appended to the restart filenames. Only done for
               filenames without absolute path. Same as '-restartpath
               dir' option.

          LPJOUTPUT
               default method for generating output files. Valid
               values are mpi2, buffer, gather. Used by the MPI
               version only. Same as '-output method' option.


     EXIT STATUS
          lpjml and lpj returns a zero exit status if the simulation
          finishes successfully.  Non zero is returned in case of
          failure.

     DIAGNOSTICS
          On error the program prints the following message on stderr:

          ERRORxxx: message, program terminated unsuccessfully

          where xxx is the return code of the program. The following
          error codes are defined:

          ERROR001
               Error reading configuration. Check syntax of
               configuration file.

          ERROR002
               Error initializing climate. Check whether all input
               files are present.

          ERROR003
               Error initializing land use, check for missing input
               file.

          ERROR004
               Error initializing water use, check for missing input
               file.

          ERROR005
               Error initializing grid, check for missing input files.

          ERROR006
               Error initializing drainage, check for missing input
               files.

          ERROR007
               Invalid carbon balance. Internal error

          ERROR008
               Invalid water balance. Internal error

          ERROR009
               Negative discharge. Internal error

          ERROR010
               Negative fire probability. Internal error.

          ERROR011
               Negative soil moisture. Internal error

          ERROR012
               Error allocating memory. Rerun parallel program on more
               MPI tasks to reduce memory per task.

          ERROR013
               Negative stand fraction. Internal error.

          ERROR014
               Stand fraction sum error. Can be caused by invalid
               restart file.

          ERROR015
               List is empty in dellistitem. Internal error.

          ERROR016
               Index out of range in dellistitem. Internal error

          ERROR017
               Error in newlanduse. Can be caused by invalid restart
               file.

          ERROR018
               Invalid year in 'getco2'. CO2 data file is too short.

          ERROR019
               Crop fraction >1. Internal error.

          ERROR020
               No natural stand for deforest. Internal error.

          ERROR021
               Wrong cultivation type. Internal error.

          ERROR022
               Invalid discharge. Internal error.

          ERROR023
               Cannot allocate buffer memory. Rerun program with
               option '-output mpi2' or '-output gather'. The total
               amount of memory allocated for the output buffers can
               be obtained by invoking lpjcheck. The buffer size has
               to be divided by the number of MPI tasks.

          ERROR024
               PFT list is not empty in setaside. Internal error.

          ERROR025
               Negative establishment rate. Internal error.

          ERROR026
               Floating point error occurred. Floating point
               exceptions will only be thrown if -fpe option is set.
               This is in particular useful if NaNs appear in the
               output files.  Internal error.

          Internal errors will generate a core dump and have to be
          fixed by changes in the code. A "post-mortem" analysis can
          be made by calling

          gdb $LPJROOT/bin/lpjml core

          It is recommended to compile the code without optimization
          and inlining making the inspection of the core file easier.
          Configure in $LPJROOT with

          configure.sh -debug
          make clean
          make

          will do the job. If no core file is generated set the user
          limit for core files:

          ulimit -c unlimited

          Some of these errors are only raised if the -DSAFE flag has
          been set in Makefile.inc. The flags set at compile time can
          be obtained by invoking lpjml -v.


     AUTHORS
          Werner von Bloh (Werner.von.Bloh@pik-potsdam.de), Sibyll
          Schaphoff (Sibyll.Schaphoff@pik-potsdam.de), Stefanie Rost
          (Jachner) (Stefanie.Rost@pik-potsdam.de), Marlies
          Gumpenberger (Marlies.Gumpenberger@pik-potsdam.de), Tim
          Beringer (Erbrecht) (Tim.Beringer@pik-potsdam.de), Christoph
          Mueller (Christoph.Mueller@pik-potsdam.de)


     SEE ALSO
          lpjsubmit(1), lpjcheck(1), cru2clm(1), txt2clm(1),
          grid2clm(1), cft2clm(1), lpjdistribute(1),
          lpjdistribute_river(1), lpjcat(1), lpjprint(1),
          printheader(1), cat2bsq(1), output_bsq(1), lpj_paths.sh(1),
          lpj_paths.csh(1), newpft.sh(1), lpjml.conf(5), lpj.conf(5),
          clm(5)

          The LPJ & LPJmL Web Distribution Portal:
               http://www.pik-potsdam.de/lpj



































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