28 Models in PEcAn

28.1 BioCro Configuration

BioCro uses a config.xml file similar to ED2. At this time, no other template files are required.

28.2 BioCro

Model Information
Home Page
Source Code
License
Authors
PEcAn Integration

Introduction

Introduction about model

PEcAn configuration file additions

Should list the model specific additions to the PEcAn file here

Model specific input files

List of inputs required by model, such as met, etc.

Model configuration files

BioCro uses a config.xml file similar to ED2. At this time, no other template files are required.

Installation notes

This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.

28.3 CLM

Model Information
Home Page
Source Code
License
Authors
PEcAn Integration

Introduction

Introduction about model

PEcAn configuration file additions

Should list the model specific additions to the PEcAn file here

Model specific input files List of inputs required by model, such as met, etc.

Model configuration files

MODEL is configured using 3 files which are placed in the run folder, as well as a symbolic link to the met file.

file1 : template for this file is located at models/MODEL/inst/file1 and is not modified.
file2 : template for this file is located at models/MODEL/inst/file2 and is not modified.
file3 : template for this file is in models/MODEL/inst/file3 or it is specified in the <model> section as <template>. The values in this template are replaced by those computed in the earlier stages of PEcAN.

Installation notes

This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.

28.4 DALEC

Model Information
Home Page
Source Code
License
Authors
PEcAn Integration

Introduction

Introduction about model

PEcAn configuration file additions

Should list the model specific additions to the PEcAn file here

Model specific input files

List of inputs required by model, such as met, etc.

Model configuration files

MODEL is configured using 3 files which are placed in the run folder, as well as a symbolic link to the met file.

file1 : template for this file is located at models/MODEL/inst/file1 and is not modified.
file2 : template for this file is located at models/MODEL/inst/file2 and is not modified.
file3 : template for this file is in models/MODEL/inst/file3 or it is specified in the <model> section as <template>. The values in this template are replaced by those computed in the earlier stages of PEcAN.

Installation notes

This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.

28.5 ED

Model Information
Home Page	http://moorcroftlab.oeb.harvard.edu/
Source Code	https://github.com/EDmodel/ED2
License
Authors	Paul Moorcroft, …
PEcAn Integration	Michael Dietze, Rob Kooper

Introduction

Introduction about ED model

PEcAn configuration file additions

Should list the model specific additions to the PEcAn file here

Model specific input files

List of inputs required by model, such as met, etc.

Model configuration files

ED2 is configured using 2 files which are placed in the run folder.

ED2IN : template for this file is located at models/ed/inst/ED2IN.<revision>. The values in this template that need to be modified are described below and are surrounded with @ symbols.
config.xml : this file is generated by PEcAn. Some values are stored in the pecan.xml in <pfts><pft><constants> section as well as in <model> section.

An example of the template can be found in ED2IN.r82

The ED2IN template can contain the following variables. These will be replaced with actual values when the model configuration is written.

**@ENSNAME@** : run id of the simulation, used in template for NL%EXPNME
**@START_MONTH@** : start of simulation UTC time, from <run><start.date>, used in template for NL%IMONTHA
**@START_DAY@** : start of simulation UTC time, from <run><start.date>, used in template for NL%IDATEA
**@START_YEAR@** : start of simulation UTC time, from <run><start.date>, used in template for NL%IYEARA
**@END_MONTH@** : end of simulation UTC time, from <run><end.date>, used in template for NL%IMONTHZ
**@END_DAY@** : end of simulation UTC time, from <run><end.date>, used in template for NL%IDATEZ
**@END_YEAR@** : end of simulation UTC time, from <run><end.date>, used in template for NL%IYEARZ
**@SITE_LAT@** : site latitude location, from <run><site><lat>, used in template for NL%POI_LAT
**@SITE_LON@** : site longitude location, from <run><site><lon>, used in template for NL%POI_LON
**@SITE_MET@** : met header location, from <run><site><met>, used in template for NL%ED_MET_DRIVER_DB
**@MET_START@** : first year of met data, from <run><site><met.start>, used in template for NL%METCYC1
**@MET_END@** : last year of met data, from <run><site><met.end>, used in template for NL%METCYCF
**@PHENOL_SCHEME@** : phenology scheme, if this variabe is 1 the following 3 fields will be used, otherwise they will be set to empty strings, from <model><phenol.scheme>, used in template for NL%IPHEN_SCHEME
**@PHENOL_START@** : first year for phenology, from <model><phenol.start>, used in template for NL%IPHENYS1 and NL%IPHENYF1
**@PHENOL_END@** : last year for phenology, from <model><phenol.end>, used in template for NL%IPHENYSF and NL%IPHENYFF
**@PHENOL@** : path and prefix of the prescribed phenology data, from * <phenol>, used in template for NL%PHENPATH
**@SITE_PSSCSS@** : path and prefix of the previous ecosystem state, from <model><psscss>, used in template for NL%SFILIN
**@ED_VEG@** : path and prefix of the vegetation database, used only to determine the land/water mask, from <model><veg>, used in template for NL%VEG_DATABASE
**@ED_SOIL@** : path and prefix of the soil database, used to determine the soil type, from <model><soil>, used in template for NL%SOIL_DATABASE
**@ED_INPUTS@** : input directory with dataset to initialise chilling degrees and growing degree days, which is used to drive the cold-deciduous phenology, from <model><inputs>, used in template for NL%THSUMS_DATABASE
**@FFILOUT@** : path and prefix for analysis files, generated from <run><host><outdir>/run.id/analysis, used in template for NL%FFILOUT
**@SFILOUT@** : path and prefix for history files, generated from <run><host><outdir>/run.id/history, used in template for NL%SFILOUT
**@CONFIGFILE@** : XML file containing additional parameter settings, this is always “config.xml”, used in template for NL%IEDCNFGF
**@OUTDIR@** : location where output files are written (without the runid), from <run><host><outdir>, should not be used.
**@SCRATCH@** : local scratch space for outputs, generated /scratch/<username>/run$scratch, should not be used right now since it only works on ebi-cluster

Installation notes

This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.

** BU geo**

TACC lonestar

module load hdf5
curl -o ED.r82.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/ED.r82.tgz
tar zxf ED.r82.tgz
rm ED.r82.tgz
cd ED.r82/ED/build/bin
curl -o include.mk.lonestar http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.lonestar
make OPT=lonestar

TACC stampede

module load hdf5
curl -o ED.r82.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/ED.r82.tgz
tar zxf ED.r82.tgz
rm ED.r82.tgz
cd ED.r82/ED/build/bin
curl -o include.mk.stampede http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.stampede
make OPT=stampede

28.6 ED2 Configuration

ED2 is configured using 2 files which are placed in the run folder.

ED2IN : template for this file is located at models/ed/inst/ED2IN.<revision>. The values in this template that need to be modified are described below and are surrounded with @ symbols.
config.xml : this file is generated by PEcAn. Some values are stored in the pecan.xml in <pfts><pft><constants> section as well as in <model> section.

An example of the template can be found in ED2IN.r82

28.6.1 ED2IN configuration variables

**@ENSNAME@** : run id of the simulation, used in template for NL%EXPNME

**@START_MONTH@** : start of simulation UTC time, from <run><start.date>, used in template for NL%IMONTHA
**@START_DAY@** : start of simulation UTC time, from <run><start.date>, used in template for NL%IDATEA
**@START_YEAR@** : start of simulation UTC time, from <run><start.date>, used in template for NL%IYEARA
**@END_MONTH@** : end of simulation UTC time, from <run><end.date>, used in template for NL%IMONTHZ
**@END_DAY@** : end of simulation UTC time, from <run><end.date>, used in template for NL%IDATEZ
**@END_YEAR@** : end of simulation UTC time, from <run><end.date>, used in template for NL%IYEARZ

**@SITE_LAT@** : site latitude location, from <run><site><lat>, used in template for NL%POI_LAT
**@SITE_LON@** : site longitude location, from <run><site><lon>, used in template for NL%POI_LON

**@SITE_MET@** : met header location, from <run><site><met>, used in template for NL%ED_MET_DRIVER_DB
**@MET_START@** : first year of met data, from <run><site><met.start>, used in template for NL%METCYC1
**@MET_END@** : last year of met data, from <run><site><met.end>, used in template for NL%METCYCF

**@PHENOL_SCHEME@** : phenology scheme, if this variabe is 1 the following 3 fields will be used, otherwise they will be set to empty strings, from <model><phenol.scheme>, used in template for NL%IPHEN_SCHEME
**@PHENOL_START@** : first year for phenology, from <model><phenol.start>, used in template for NL%IPHENYS1 and NL%IPHENYF1
**@PHENOL_END@** : last year for phenology, from <model><phenol.end>, used in template for NL%IPHENYSF and NL%IPHENYFF
**@PHENOL@** : path and prefix of the prescribed phenology data, from <model><phenol>, used in template for NL%PHENPATH

**@SITE_PSSCSS@** : path and prefix of the previous ecosystem state, from <model><psscss>, used in template for NL%SFILIN
**@ED_VEG@** : path and prefix of the vegetation database, used only to determine the land/water mask, from <model><veg>, used in template for NL%VEG_DATABASE
**@ED_SOIL@** : path and prefix of the soil database, used to determine the soil type, from <model><soil>, used in template for NL%SOIL_DATABASE
**@ED_INPUTS@** : input directory with dataset to initialise chilling degrees and growing degree days, which is used to drive the cold-deciduous phenology, from <model><inputs>, used in template for NL%THSUMS_DATABASE

**@FFILOUT@** : path and prefix for analysis files, generated from <run><host><outdir>/run.id/analysis, used in template for NL%FFILOUT
**@SFILOUT@** : path and prefix for history files, generated from <run><host><outdir>/run.id/history, used in template for NL%SFILOUT

**@CONFIGFILE@** : XML file containing additional parameter settings, this is always “config.xml”, used in template for NL%IEDCNFGF

**@OUTDIR@** : location where output files are written (without the runid), from <run><host><outdir>, should not be used.
**@SCRATCH@** : local scratch space for outputs, generated /scratch/\<username\>/run$scratch, should not be used right now since it only works on ebi-cluster

ED Computation HPC

TACC lonestar

module load hdf5
curl -o ED.r82.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/ED.r82.tgz
tar zxf ED.r82.tgz
rm ED.r82.tgz
cd ED.r82/ED/build/bin
curl -o include.mk.lonestar http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.lonestar
make OPT=lonestar

TACC stampede

module load hdf5
curl -o ED.r82.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/ED.r82.tgz
tar zxf ED.r82.tgz
rm ED.r82.tgz
cd ED.r82/ED/build/bin
curl -o include.mk.stampede http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.stampede
make OPT=stampede

28.7 GDAY

Model Information
Home Page
Source Code
License
Authors
PEcAn Integration

Introduction

Introduction about model

PEcAn configuration file additions

Should list the model specific additions to the PEcAn file here

Model specific input files

List of inputs required by model, such as met, etc.

Model configuration files

MODEL is configured using 3 files which are placed in the run folder, as well as a symbolic link to the met file.

file1 : template for this file is located at models/MODEL/inst/file1 and is not modified.
file2 : template for this file is located at models/MODEL/inst/file2 and is not modified.
file3 : template for this file is in models/MODEL/inst/file3 or it is specified in the <model> section as <template>. The values in this template are replaced by those computed in the earlier stages of PEcAN.

Installation notes

This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.

28.8 LINKAGES

Model Information
Home Page
Source Code
License
Authors
PEcAn Integration

Introduction

Introduction about model

PEcAn configuration file additions

Should list the model specific additions to the PEcAn file here

Model specific input files

List of inputs required by model, such as met, etc.

Model configuration files

MODEL is configured using 3 files which are placed in the run folder, as well as a symbolic link to the met file.

file1 : template for this file is located at models/MODEL/inst/file1 and is not modified.
file2 : template for this file is located at models/MODEL/inst/file2 and is not modified.
file3 : template for this file is in models/MODEL/inst/file3 or it is specified in the <model> section as <template>. The values in this template are replaced by those computed in the earlier stages of PEcAN.

Installation notes

This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.

28.9 LPJ-GUESS

Model Information
Home Page
Source Code
License
Authors
PEcAn Integration

Introduction

Introduction about model

PEcAn configuration file additions

Should list the model specific additions to the PEcAn file here

Model specific input files

List of inputs required by model, such as met, etc.

Model configuration files

MODEL is configured using 3 files which are placed in the run folder, as well as a symbolic link to the met file.

file1 : template for this file is located at models/MODEL/inst/file1 and is not modified.
file2 : template for this file is located at models/MODEL/inst/file2 and is not modified.
file3 : template for this file is in models/MODEL/inst/file3 or it is specified in the <model> section as <template>. The values in this template are replaced by those computed in the earlier stages of PEcAN.

Installation notes

This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.

28.10 MAESPA

Model Information
Home Page	http://maespa.github.io/
Source Code	http://maespa.github.io/download.html
License
Authors	Belinda Medlyn and Remko Duursma
PEcAn Integration	Tony Gardella, Martim DeKauwe, Remki Duursma

Introduction

PEcAn configuration file additions

Model specific input files

Model configuration files

MODEL is configured using 3 files which are placed in the run folder, as well as a symbolic link to the met file.

file1 : template for this file is located at models/MODEL/inst/file1 and is not modified.
file2 : template for this file is located at models/MODEL/inst/file2 and is not modified.
file3 : template for this file is in models/MODEL/inst/file3 or it is specified in the <model> section as <template>. The values in this template are replaced by those computed in the earlier stages of PEcAN.

Installation notes

Installing the MAESPA model requires cloning the MAESPA Bitbucket Repository, executing the makefile, and ensuring that the Maeswarp R package is correctly installed.

To clone and compile the model, execute this code at the command line

git clone https://bitbucket.org/remkoduursma/maespa.git

cd maespa

make clean

make

maespa.out is your executable. Example input files can be found in the inputfiles directory. Executing measpa.out from within one of the example directories will produce output.

MAESPA developers have also developed a wrapper package called Maeswrap. The usual R package installation method install.packages may present issues with downloading an unpacking a dependency package called rgl. Here are a couple of solutions:

Solution 1

From the Command Line

sudo apt-get install r-cran-rgl

then from within R

install.packages("Maeswrap")

Solution 2

From the Command line

sudo apt-get install libglu1-mesa-dev

then from within R

install.packages("Maeswrap")

This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.