lpjml.1
NAME
lpj, lpjml - Dynamic global vegetation model with managed
land and river routing
SYNOPSIS
lpjml [-h] [-l] [-v] [-vv] [-param] [-pp cmd] [-fpe] [-image
host[:inport[,outport]]] [-wait time] [-output
{write|gather|mpi2|socket=hostname[:port]}] [-outpath dir]
[-inpath dir] [-restartpath dir] [[-Dmacro[=value]] [-Idir]
...] [filename]
lpj [-h] [-l] [-v] [-vv] [-param] [-pp cmd] [-fpe] [-image
host[:inport[,outport]]] [-wait time] [-output
{write|gather|mpi2|socket=hostname[:port]}] [-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. 5000 years to develop equilibrium vegetation
and soil structure. A restart file can be created to save
compute time for the spin-up phase. If the Message Passing
Interface (MPI) library is available a parallel version of
the program is built. If -DIMAGE flag is set in Makefile.inc
coupling the IMAGE model via the TDT library is enabled.
OPTIONS
-h print a short help text
-l print the license file
-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.
-param
print LPJmL parameter for soils and PFTs.
-pp cmd
set preprocessor program to cmd. Default is cpp -P.
-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.
-image host[:inport[,outport]]
set host where IMAGE model is running. Default is
localhost. inport and outport are the port numbers for
ingoing and outgoing data. Default port numbers are
2225 and 2224, respectively. This option is only
available for the IMAGE version of the code.
-wait time
set time to wait for connection to IMAGE model. Time is
measured in seconds. Default value is 10 sec. This
option is only available for the IMAGE version of the
code.
-output {gather|mpi2|socket=hostname[:port]]}
use the given output method to write data to disk or to
a output channel. Valid output methods are write,
gather, mpi2, and socket. The default output method for
the MPI version is gather sending all output to the
root task, while the default method is write for the
sequential version of the code. Method mpi2 uses MPI-2
parallel file functions, while output method socket
sends output data via a TCP/IP socket to a remote host
hostname. Default port is 2222. lpjliveview is a
program to display output variables on a X11 display at
run time. The mpi2 and gather output methods are 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.js for
lpjml and lpj.js for lpj.
EXAMPLES
Perform simulation with input from the /scratch file system:
lpjml -inpath /scratch/02/lpj
Perform simulation with output sent to host aix:
lpjml -output socket=aix
enabled:
Start simulation from restart file with floating point exceptions
lpjml -DFROM_RESTART -fpe lpjml.js
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. Same as '-pp' option.
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.
LPJIMAGE
sets the host where IMAGE model is running. Same as '-
image' option.
LPJWAITIMAGE
sets time to wait for connection to IMAGE model. Same
as in '-wait' option.
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, gather, and socket. 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. External error
ERROR002
Error initializing input. Check whether all input files
are present. External error
ERROR003
Error initializing grid, check for missing input files.
External error
ERROR004
Invalid carbon balance. Internal error
ERROR005
Invalid water balance. Internal error
ERROR006
Negative discharge. Internal error
ERROR007
Negative fire probability. Internal error.
ERROR008
Negative soil moisture. Internal error
ERROR009
Error allocating memory. Rerun parallel program on more
MPI tasks to reduce memory per task. External error
ERROR010
Negative stand fraction. Internal error.
ERROR011
Stand fraction sum error. Can be caused by invalid
restart file. External error
ERROR012
List is empty in dellistitem(). Internal error.
ERROR013
Index out of range in dellistitem(). Internal error
ERROR014
Error in newlanduse(). Can be caused by invalid restart
file. External error
ERROR015
Invalid year in getco2(). CO2 data file is too short.
External error
ERROR016
Crop fraction >1. Internal error.
ERROR017
No natural stand for deforest(). Internal error.
ERROR018
Wrong cultivation type. Internal error.
ERROR019
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.
ERROR021
PFT list is not empty in setaside(). Internal error.
ERROR022
Negative establishment rate. Internal error.
ERROR023
Output channel is broken. This error is only raised if
'-output socket' option is set. It is usually caused by
a premature end of the corresponding live view program.
External error.
ERROR024
Error sending data to the IMAGE model. This error can
only be raised if LPJmL is compiled with the -DIMAGE
flag set in Makefile.inc. External error.
ERROR025
Error opening connection to IMAGE model. This error can
only be raised if LPJmL is compiled with the -DIMAGE
flag set in Makefile.inc. External error.
ERROR026
Not enough setaside stand created to put the reservoir.
Internal error.
ERROR027
Forest left after deforestation. Internal error.
ERROR028
Outflow reservoir error. Internal error.
ERROR029
Error in permafrost module. Internal error.
ERROR030
Error in global water balance. Internal error.
ERROR031
Error in store climate function.
ERROR032
No FMS coupler supported.
ERROR033
Error initializing soil temperature
ERROR034
Invalid radiation model. 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. After the core file has
been created a backtrace of the failed program can be
obtained by calling
backtrace
Without any arguments lpjml will be inspected and the call
tree displayed using the core file in the working directory.
AUTHORS
For authors and contributors see AUTHORS file
COPYRIGHT
(C) Potsdam Institute for Climate Impact Research (PIK), see
COPYRIGHT file
SEE ALSO
lpjsubmit(1), lpjcheck(1), configure.sh(1), backtrace(1),
cru2clm(1), txt2clm(1), grid2clm(1), cft2clm(1), lpjcat(1),
lpjprint(1), printharvest(1), printclm(1), printheader(1),
cat2bsq(1), output_bsq(1), lpj_paths.sh(1),
lpj_paths.csh(1), lpjml.conf(5), lpj.conf(5),
lpjml_image.conf(5), clm(5)
Contact: https://github.com/PIK-LPJmL/LPJmL /lpjml
Man(1) output converted with
man2html