28 Template MODEL page

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.

VM

28.1 Template MODEL page

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.

VM

28.2 BioCro Configuration

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

28.3 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.

VM

28.4 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.

VM

28.5 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.

VM

28.6 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

28.6.1 Introduction

Introduction about ED model

28.6.2 PEcAn configuration file additions

The following sections of the PEcAn XML are relevant to the ED model:

  • model
    • id – BETY model ID. Each ID corresponds to a different revision of ED (see below)
    • revision – The revision (a.k.a. release) number of ED (e.g. “r82”). “rgit” indicates the latest code on the ED repository.
    • edin – Name of the template ED2IN configuration file. If this is a functional path that points to a specific file, that file is used. If no file is found following the path literally, the workflow will try the path relative to the PEcAn.ED2 package using system.file (recall that files in inst are moved in the package root, but all other directory structure is preserved). If this is omitted, PEcAn.ED2::write.configs.ED2 will look for a file called ED2IN.<revision> (e.g. ED2IN.rgit, ED2IN.r86) in the PEcAn.ED2 package.
      • Example: <edin>ED2IN.rgit</edin> will use the ED2IN.rgit file shipped with PEcAn.ED2 regardless of the revision of ED used. (Note however that if a file called ED2IN.rgit exists in the workflow runtime directory, that file will be used instead).
    • start.date, end.date – Run start and end date, respectively
    • met.start, met.end – Start and end year of meteorology inputs. By default (if omitted), these are set to the years of start.date and end.date, respectively. Setting these values to a shorter interval than start.date and end.date will cause ED to loop the meteorology input over the specified years. This may be useful for, for example, spinning up ED under a set of constant climate conditions.
    • phenol.scheme
    • phenol
    • phenol.start
    • phenol.end

    • ed2in_tags – Named list of additional tags in the ED2IN to be modified. These modifications override any of those set by other parts of the PEcAn workflow. These tags must be in all caps. Any tags that are not already in the ED2IN file will be added; this makes this an effective way to run newer versions of ED2 that have new ED2IN parameters without having to provide an entire new ED2IN. For example:

      <model>
  <ed2in_tags>
    <IOOUTPUT>0</IOOUTPUT>
    <PLANT_HYDRO_SCHEME>0</PLANT_HYDRO_SCHEME>
    <ISTOMATA_SCHEME>0</ISTOMATA_SCHEME>
    <ISTRUCT_GROWTH_SCHEME>0</ISTRUCT_GROWTH_SCHEME>
    <TRAIT_PLASTICITY_SCHEME>0</TRAIT_PLASTICITY_SCHEME>
  </ed2in_tags>
</model>
    • barebones_ed2in – Whether or not to try to annotate the ED2IN file with comments. If “true”, skip all comments and only write the tags themselves. If “false” (default), try to transfer comments from the template file into the target file.
    • jobtemplate
    • prerun – String of commands to be added to the job.sh model execution script before the model is run. Multiple commands should be separated by proper bash syntax – i.e. either with && or ;.

      • One common use of this argument is to load modules on some HPC systems – for instance:

        <prerun>module load git hdf5</prerun>

      • If your particular version of ED is failing early during execution with a mysterious “Segmentation fault”, that may indicate that its process is exceeding its stack limit. In this case, you may need to remove the stack limit restriction with a prerun command like the following:

        <prerun>ulimit -s unlimited</prerun>
    • postrun – Same as <prerun>, but for commands to be run after model execution.
    • binary – The full path to the ED2 binary on the target machine.
    • binary_args – Additional arguments to be passed to the ED2 binary. Some common arguments are:
      • -s – Delay OpenMPI initialization until the last possible moment. This is needed when running ED2 in a Docker container. It is included by default when the host is rabbitmq.
      • -f /path/to/ED2IN – Full path to a specific ED2IN namelist file. Typically, this is not needed because, by default, ED searches for the ED2IN in the current directory and the PEcAn workflow places the ED2IN file and a symbolic link to the ED executable in the same (run) directory for you.
  • run/site
    • lat – Latitude coordinate of site
    • lon – Longitude coordinate of site
  • inputs
    • met/path – Path to ED_MET_DRIVER_HEADER file
    • pss: [required] location of patch file
    • css: [required] location of cohort file
    • site: [optional] location of site file
    • lu: [required] location of land use file
    • thsums: [required] location of thermal sums file
    • veg: [required] location of vegetation data
    • soil: [required] location of soil data

28.6.3 Model specific input files

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

28.6.4 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 * <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

28.6.5 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.

28.6.5.1 VM

28.6.5.2 BU geo

28.6.5.3 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

28.6.5.4 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.

VM

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.

VM

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.

VM

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.

VM

28.11 PRELES

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.

VM

28.12 SIPNET configuration

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

  • sipnet.in : template for this file is located at models/sipnet/inst/sipnet.in and is not modified.
  • sipnet.param-spatial : template for this file is located at models/sipnet/inst/template.param-spatial and is not modified.
  • sipnet.param : template for this file is in models/sipnet/inst/template.param or it is specified in the <model> section as <default.param>. The values in this template are replaced by those computed in the earlier stages of PEcAN.

28.13 Sipnet

Model Information
Home Page
Source Code
License
Authors
PEcAn Integration Michael Dietze, Rob Kooper

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

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

  • sipnet.in : template for this file is located at models/sipnet/inst/sipnet.in and is not modified.
  • sipnet.param-spatial : template for this file is located at models/sipnet/inst/template.param-spatial and is not modified.
  • sipnet.param : template for this file is in models/sipnet/inst/template.param or it is specified in the <model> section as <default.param>. 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.

SIPNET version unk:

if [ ! -e ${HOME}/sipnet_unk ]; then
  cd
  curl -o sipnet_unk.tar.gz http://isda.ncsa.illinois.edu/~kooper/PEcAn/models/sipnet_unk.tar.gz
  tar zxf sipnet_unk.tar.gz
  rm sipnet_unk.tar.gz
fi
cd ${HOME}/sipnet_unk/
make clean
make
sudo cp sipnet /usr/local/bin/sipnet.runk
make clean

SIPNET version 136:

if [ ! -e ${HOME}/sipnet_r136 ]; then
  cd
  curl -o sipnet_r136.tar.gz http://isda.ncsa.illinois.edu/~kooper/EBI/sipnet_r136.tar.gz
  tar zxf sipnet_r136.tar.gz
  rm sipnet_r136.tar.gz
  sed -i 's#$(LD) $(LIBLINKS) \(.*\)#$(LD) \1 $(LIBLINKS)#' ${HOME}/sipnet_r136/Makefile
fi
cd ${HOME}/sipnet_r136/
make clean
make
sudo cp sipnet /usr/local/bin/sipnet.r136
make clean

VM

28.13.1 Download GFDL

The Downlad.GFDL function assimilates 3 hour frequency CMIP5 outputs generated by multiple GFDL models. GFDL developed several distinct modeling streams on the timescale of CMIP5 and AR5. These models include CM3, ESM2M and ESM2G with a spatial resolution of 2 degrees latitude by 2.5 degrees longitude. Each model has future outputs for the AR5 Representative Concentration Pathways ranging from 2006-2100.

28.13.2 CM3

GFDL’s CMIP5 experiments with CM3 included many of the integrations found in the long-term CMIP5 experimental design. The focus of this physical climate model is on the role of aerosols, aerosol-cloud interactions, and atmospheric chemistry in climate variability and climate change.

28.13.3 ESM2M & ESM2G

Two new models representing ocean physics with alternative numerical frameworks to explore the implications of some of the fundamental assumptions embedded in these models. Both ESM2M and ESM2G utilize a more advanced land model, LM3, than was available in ESM2.1 including a variety of enhancements (Milly et al., in prep). GFDL’s CMIP5 experiments with Earth System Models included many of the integrations found in the long-term CMIP5 experimental design. The ESMs, by design, close the carbon cycle and are used to study the impact of climate change on ecosystems, ecosystem changes on climate and human activities on ecosystems.

For more information please navigate here

CM# ESM2M ESM2G
rcp26 r1i1p1 r1i1p1
rcp45 r1i1p1, r3i1p1,r5i1p1 r1i1p1 r1i1p1
rcp60 r1i1p1 r1i1p1
rcp85 r1i1p1 r1i1p1 r1i1p1