User's guide to the NCAR Community Atmosphere Model (CAM 3.0

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Content: June 2004
User's Guide to the NCAR Community Atmosphere Model (CAM 3.0)
James R. McCaa Mathew Rothstein Brian E. Eaton James M. Rosinski Erik Kluzek Mariana Vertenstein
Climate And Global Dynamics Division National Center For Atmospheric Research Boulder, Colorado, USA
Climate And Global Dynamics Division National Center For Atmospheric Research Boulder, Colorado
The National Center for Atmospheric Research (NCAR) is operated by the University Corporation for Atmospheric Research (UCAR) and is sponsored by the National Science Foundation. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Contents
Acknowledgments
ix
1 Introduction
1
1.1 How to Use This Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Quick Start . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3 Changes since CAM 2.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.4 Obtaining and unpacking the source code and datasets . . . . . . . . . . . . . . 3
1.4.1 CAM input dataset directory hierarchy . . . . . . . . . . . . . . . . . . . 3
1.4.2 CAM source code directory hierarchy . . . . . . . . . . . . . . . . . . . . 4
1.5 Getting Help ­ Other User Resources . . . . . . . . . . . . . . . . . . . . . . . . 5
1.5.1 The CAM Web Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.5.2 The cam-users mailing list . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.5.3 Reporting bugs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2 Building and Running CAM
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2.1 The configure utility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.1.1 Options to configure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.1.2 Environment variables used by configure . . . . . . . . . . . . . . . . . . 16
2.2 The build-namelist utility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.2.1 Options to build-namelist . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.2.2 Environment variables used by build-namelist . . . . . . . . . . . . . . . 19
2.3 Use Cases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.3.1 Configuring and running the default CAM executable . . . . . . . . . . . 20
2.3.2 Using the Slab Ocean Model (SOM) . . . . . . . . . . . . . . . . . . . . 22
2.4 Sample Run Scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.4.1 Use of C preprocessor tokens . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.4.2 Details of the gmake procedure . . . . . . . . . . . . . . . . . . . . . . . 25
2.5 Model Input Datasets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
2.5.1 Atmosphere Component Datasets . . . . . . . . . . . . . . . . . . . . . . 28
2.5.2 Ocean Component Datasets . . . . . . . . . . . . . . . . . . . . . . . . . 31
2.5.3 Sea-Ice Component Datasets . . . . . . . . . . . . . . . . . . . . . . . . . 32
2.5.4 Land Component Datasets . . . . . . . . . . . . . . . . . . . . . . . . . . 32
2.6 Troubleshooting Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
2.7 Running CAM as part of the CCSM coupled model system . . . . . . . . . . . . 35
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3 Model Output
37
3.1 Model History Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
3.1.1 Master Field List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
3.1.2 History Files 2 through 6 . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
3.1.3 Changing the characteristics of history files . . . . . . . . . . . . . . . . . 48
3.1.4 Naming the History Files . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
3.2 Model generated initial condition dataset files . . . . . . . . . . . . . . . . . . . 49
3.3 Restart Datasets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
3.4 Mass Store Archiving . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
3.5 Model Vertical Coordinate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
4 Simple Code Modifications
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4.1 Using the Scripts with Modified Code . . . . . . . . . . . . . . . . . . . . . . . . 53
4.2 Adding New Output Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
4.3 Trouble-Shooting Model Changes . . . . . . . . . . . . . . . . . . . . . . . . . . 54
4.3.1 Resource Allocation Errors . . . . . . . . . . . . . . . . . . . . . . . . . . 54
4.3.2 Coding Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
4.4 Porting the model to new resolutions . . . . . . . . . . . . . . . . . . . . . . . . 55
Appendices
A Glossary
57
B CAM Namelist Variables
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B.1 CAMEXP run type namelist variables . . . . . . . . . . . . . . . . . . . . . . . 61
B.2 CAMEXP time management namelist variables . . . . . . . . . . . . . . . . . . 61
B.3 CAMEXP input dataset namelist variables . . . . . . . . . . . . . . . . . . . . . 62
B.4 CAMEXP history file namelist variables . . . . . . . . . . . . . . . . . . . . . . 62
B.5 CAMEXP mass store control namelist variables . . . . . . . . . . . . . . . . . . 62
B.6 CAMEXP restart file namelist variables . . . . . . . . . . . . . . . . . . . . . . 62
B.7 CAMEXP dynamics namelist variables . . . . . . . . . . . . . . . . . . . . . . . 62
B.8 CAMEXP physics namelist variables . . . . . . . . . . . . . . . . . . . . . . . . 62
B.9 CAMEXP non-water constituent namelist variables . . . . . . . . . . . . . . . . 62
B.10 CAMEXP memory namelist variables . . . . . . . . . . . . . . . . . . . . . . . . 63
B.11 CAMEXP performance tuning namelist variables . . . . . . . . . . . . . . . . . 63
B.12 CAMEXP orbital parameter namelist variables . . . . . . . . . . . . . . . . . . 63
B.13 Complete list of CAM namelist variables . . . . . . . . . . . . . . . . . . . . . . 63
C CLM namelist variables
79
D Details of the configuration files
81
D.1 Filepath . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
D.2 misc.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
D.3 params.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
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D.4 preproc.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 D.5 config cache.xml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 D.6 Makefile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
References
84
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List of Figures 3.1 Hybrid vertical coordinate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 v
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List of Tables 1.1 CAM Input Dataset Directory Hierarchy . . . . . . . . . . . . . . . . . . 3 1.2 CAM Source Code Directory Hierarchy . . . . . . . . . . . . . . . . . . . 4 2.1 Command line arguments to configure . . . . . . . . . . . . . . . . . . . . 9 2.2 Environment variables used by configure . . . . . . . . . . . . . . . . . . . 16 2.3 Command line arguments to build-namelist . . . . . . . . . . . . . . . . . 17 2.4 Environment variables used by build-namelist . . . . . . . . . . . . . . . 20 2.5 Atmospheric Component Initial Dataset Fields . . . . . . . . . . . . . . . 29 2.6 Optional Atmospheric component initial dataset fields (representing "fast" processes) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 3.1 Master Field List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 4.1 Units of History File Fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 B.1 CAMEXP namelist variables . . . . . . . . . . . . . . . . . . . . . . . . . . 63 C.1 CLMEXP namelist variables . . . . . . . . . . . . . . . . . . . . . . . . . . 79 D.1 misc.h pre-processor tokens . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 D.2 params.h pre-processor tokens . . . . . . . . . . . . . . . . . . . . . . . . . . 83 D.3 preproc.h pre-processor tokens . . . . . . . . . . . . . . . . . . . . . . . . . 83 vii
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Acknowledgments The authors wish to acknowledge the many members of NCAR's Climate Modeling Section (CMS) and Computer Software and Engineering Group (CSEG) who have contributed to this document over the years. The new model would not exist without the significant input from members of the CCSM Atmospheric Model Working Group AMWG too numerous to mention. Bill Collins (NCAR), Leo Donner (GFDL), James Hack (NCAR), David Randall (Colorado State University), and Phil Rasch (NCAR) were the co-chairs of the AMWG during the development of CAM 3.0. We would also like to acknowledge the substantial contributions to the CAM 3.0 effort from the National Science Foundation, Department of Energy, the National Oceanic and Atmospheric Administration, and the National Aeronautics and Space Administration. ix
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Chapter 1 Introduction The Community Atmosphere Model (CAM 3.0) is the latest in a series of global atmosphere models developed at the National Center for Atmospheric Research (NCAR). This guide is intended to instruct the novice user on running CAM 3.0 and to inform the more experienced user on the changes that have gone into CAM 3.0 from CAM 2.0. CAM 3.0 contains significant scientific and software changes from the last major release (CAM 2.0). These are discussed below in section 1.3. Please see the CAM 3.0 Scientific Descriptions [Collins et al., 2004] for a detailed discussion of the science in the model. Note that the climate produced by this version of the model is considerably different than that of the CAM 2.0 release. 1.1 How to Use This Document If you're just anxious to get a model run started and want to sort out the details later, jump to the section named Quick Start (1.2). The novice user should learn how to obtain the source code and datasets (see section 1.4) and then go to Building and Running CAM (2) and read the details of how to build and run the model. The novice user would also do well to experiment with the different use cases presented in Use Cases (2.3) before they go on to their own work. The glossary will also be useful for the novice user to understand the terms and abbreviations used in this guide. An experienced user of CAM should read Section 1.3, describing changes since CAM 2.0, and may wish to to reference the various tables on namelist items, output fields, etc. A user who also needs to make code changes will want to study the DRAFT Interface to Column Physics and Chemistry Packages, which gives some guidance on making changes to the model. When the CAM 3.0 Developer's Guide is complete, it will give more detail on the model internals and how the user would approach making more extensive changes. An experienced user who has also developed their own build/run mechanism may also be interested in the details of the configuration files given in the appendix. If you have the pdf or html versions of this document, please note the use of hyperlinks in the presented examples ­ in many cases you can click on namelist variables or command line option and go right to a description of the item in the relevant table. Lastly, throughout the document this font is used to indicate shell commands and options, fragments of code, namelist variables, etc. Where examples from an inter- 1
active C shell session are presented, lines starting with % indicate the shell prompt. 1.2 Quick Start The following list of steps allows a user to quickly make a one day test run of CAM 3.0. 1. Download the CAM source code, resolution-independent datasets, and T42 datasets from: http://www.ccsm.ucar.edu/php/ccsmAgreement.php?indexId=36. You will need to accept the CAM License Agreement. 2. Untar each dataset: % gunzip -c cam3.0 source code.tar.gz | tar xvf % gunzip -c cam3.0 forall datasets.tar.gz | tar xvf % gunzip -c cam3.0 64x128 T42 datasets.tar.gz | tar xvf - 3. Set the environment variable "CSMDATA" to the location of the input datasets: % setenv CSMDATA `pwd` 4. Execute the configure command: % ./cam1/models/atm/cam/bld/configure 5. Build cam: % gmake 6. Execute the build-namelist command: % ./cam1/models/atm/cam/bld/build-namelist 7. Run cam: % ./cam < namelist At this point CAM should run for one day and exit. For more sophisticated runs you will surely want to read the sections titled Use Cases (2.3) and Sample Run Scripts (2.4). 1.3 Changes since CAM 2.0 Highlights of the software improvements include: · Performance improvements for all three dynamical cores in the areas of: ­ load balancing ­ interprocess communication ­ physics and dynamics decompositions ­ compiler optimizations ­ memory requirements ­ vectorization · Inclusion of a single column model (SCAM). · New run-time controls for performance and science options. · Ability to output a contiguous subset of columns to the history tape instead of a full field. New science developments include: 2
· Updated parameterizations for prognostic cloud water, cloud ice, precipitation, and cloud fraction. · Inclusion of a Slab Ocean Model (SOM). · Inclusion of ISCCP cloud simulator to simulate ISCCP statistical cloud diagnostics. · Diagnostic treatment of aerosols (sulfate, dust, sea salt, carbon, and volcanic). · Optional prognostic treatment of sulfate aerosols. · Improved energy conservation. · Modifications to longwave interaction with water vapor. · Updates to shortwave scheme for trace gas absorption · Atmosphere-land interface now supports rain and snow phases.
1.4 Obtaining and unpacking the source code and datasets The primary distribution mechanism for CAM is the via the CAM web page (http://www.ccsm.ucar.edu/models/atm-cam). Once there, you must follow the download link and accept the CAM distribution license. At the least you must download the "CAM 3.0 Source distribution", the "Resolutionindependent datasets", and the dataset tarball for at least one resolution. To untar the source code tar file you execute the following command: gunzip -c cam3.0 source code.tar.gz | tar xvf To untar one or more dataset tarfiles you must first go a directory that will be the dataset root directory. For all of the examples in this document it will be assumed that the environment variable CSMDATA will be set to the full pathname of this directory. You can achieve this in an interactive shell by typing the following command while in the dataset root directory: setenv CSMDATA `pwd` Now unpack each of the dataset tar files using: gunzip -c | tar xvf Note: All dataset tarfiles should be unpacked in the same directory.
1.4.1 CAM input dataset directory hierarchy The directory structure of the input datasets is as follows: Table 1.1: CAM Input Dataset Directory Hierarchy
Directory name inputdata inputdata/atm inputdata/atm/cam2 inputdata/atm/cam2/ggas inputdata/atm/cam2/inic inputdata/atm/cam2/ozone
Synopsis Top level directory where CSMDATA points to Datasets for atmosphereic models Datasets specifically for CAM Greenhouse gas forcing datasets Atmosphereic initial condition datasets Ozone datasets
3
Directory name inputdata/atm/cam2/rad inputdata/atm/cam2/scam inputdata/atm/cam2/scyc inputdata/atm/cam2/sst inputdata/lnd inputdata/lnd/clm2 inputdata/lnd/clm2/pftdata inputdata/lnd/clm2/rawdata inputdata/lnd/clm2/srfdata/cam inputdata/lnd/clm2/inidata 2.1/cam
Synopsis Radiation datasets Single column model datasets Sulfate forcing datasets Sea Surface temperature datasets Datasets for land models Datasets for CLM Plant Physiology datasets High resolution surface datasets Time-invariant surface datasets Land-model initial condition datasets
1.4.2 CAM source code directory hierarchy The directory hierarchy for CAM 3.0 is as follows. The directory hierarchy closely parallels the directory hierarchy for CCSM3 and as such seperates code out by model component. Table 1.2: CAM Source Code Directory Hierarchy
Directory name models/atm/cam/bld/ models/atm/cam/src/ models/atm/cam/src/advection/slt models/atm/cam/src/control models/atm/cam/src/dynamics/eul models/atm/cam/src/dynamics/fv models/atm/cam/src/dynamics/sld models/atm/cam/src/ocnsice/dom models/atm/cam/src/ocnsice/som models/atm/cam/src/physics/cam1 models/atm/cam/src/utils models/atm/cam/tools/ models/atm/cam/tools/cprnc models/atm/cam/tools/scam
Synopsis Scripts to build and execute the model Atmosphere model main source code directory Semi-Lagrangian Transport advection routines Control code Eulerian dynamics Finite-Volume dynamics Semi-Lagrangian dynamics Data Ocean Model Slab Ocean Model Physics routines (e.g., radiation, convection) CAM specific utilities Directory of tools (such as history compare routines) History file comparison program. Normally used to compare code modifications to a "base-line" code. Prints out summary of differences. Single column model
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Directory name models/csm share/shr models/lnd/clm2 models/ice/csim4 models/utils models/utils/esmf models/utils/pilgrim models/utils/timing
Synopsis Code shared by all the geophysical model components of the Community Climate System Model (CCSM) (e.g. code for CCSM message passing and orbital calculations) Community Land Model (CLM2.1) code Community Sea-Ice Model (CSIM4) code Independent utility codes General purpose Earth System Modeling Framework (ESMF) utilities. Parallel Library for Grid Manipulations. General purpose timing library
1.5 Getting Help ­ Other User Resources 1.5.1 The CAM Web Page The central source for information on CAM is the CAM web page (http://www.ccsm.ucar.edu/models/atm-cam). Here you can find model updates, bug reports, the latest documentation, and much, much more. Visit today! 1.5.2 The cam-users mailing list The cam-users discussion group is an open e-mail forum for rapid exchange of information, ideas, and topics of interest relating to the various versions of the NCAR CAM. This includes sharing software tools, datasets, programming tips and examples, as well as discussions of questions, problems and workarounds. The primary motivation for the establishment of this list is to facilitate and encourage communication between the users of the CAM around the world. This mail group will also be used to distribute announcements related to the CAM. To subscribe to this user group go to http://mailman.ucar.edu/mailman/listinfo/cam-users. 1.5.3 Reporting bugs If a user should encounter bugs in the code (i.e., it doesn't behave in a way in which the documentation says it should), the problem should be reported electronically to The camusers mailing list (1.5.2). When reporting a suspected bug, please include the following information: 1) the architecture on which the code was built; 2) the configuration cache xml file; 3) the namelist input; and 4) Model printout. Please note that that CAM 3.0 is a research model, and not all features are supported.
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Chapter 2 Building and Running CAM This chapter describes how to build and run the standalone model CAM 3.0. This includes a description of the build procedure, a variety of example use cases demonstrating available options, and a discussion of running the executable. CAM 3.0 may also be run as part of the Community Climate System Model (CCSM); this is discussed in Section 2.7 on page 35. Building and running CAM takes place in the following steps: 1. Configure 2. Build model 3. Build namelist 4. Execute model Configure includes setting the compile-time parameters such as resolution, dynamical core (Eulerian Spectral, Semi-Lagrangian Spectral, or Finite-Volume), type of parallelism to employ (shared-memory and/or distributed memory), number of constituents, and number of vertical levels. This step is done most easily by invoking the configure script that creates the files necissary for the build step to take place. The configure utility is discussed in the ?? (??) section. Build model includes compiling and linking the executable using the GNU make utility. The configure script creates a copy of the Makefile in the directory where the build is to take place. The user then need only change to this directory and execute gmake. Build namelist includes executing the build-namelist script, which supports a variety of options to control the run-time behavior of the model. The build-namelist utility is discussed in the The build-namelist utility (2.2) section. Execute model includes the actual invocation of the executable. When running using distributed memory parallelism this step requires knowledge of how your machine invokes MPI executables. When using shared-memory parallelism using Open-MP you may also set the number of Open-MP threads. It is assumed that the user has access to the utilities tar, gunzip, gmake (GNU make), and perl. The scripts written in perl need at least Perl 5.4 to work. Lastly, we assume there is a CAM 3.0distribution (with root $CAM ROOT) available. The most basic execution procedure is: $CAM ROOT/models/atm/cam/bld/configure gmake 7
$CAM ROOT/models/atm/cam/bld/build-namelist ./cam < namelist Most users will encapsulate these steps in higher level perl or shell scripts. Sample scripts to use as templates for this purpose are included in the directory $CAM ROOT/models/atm/cam/bld. These are discussed in more detail in the section named Sample Run Scripts (2.4). 2.1 The configure utility The configure utility provides a flexible way to specify a particular configuration of CAM. By default it will produce the configuration files required to build the standard production version of CAM (currently Eulerian dynamics at T42 spectral resolution with 26 levels). configure produces the configuration build files Filepath, misc.h, params.h, preproc.h, and Makefile. Each of these files specify compile-time parameters and settings needed to build the model. In addition, a configuration cache file (config cache.xml by default) is written which may be used in a subsequent invocation of configure to exactly reproduce the configuration files. The files produced by running configure are written to the directory where CAM will be built, which by default is the directory from which configure is executed, but can be specified to be elsewhere (see the -cam bld option). configure will optionally perform tests to validate that the Fortran compiler is operational and Fortran 90 compliant, and that the linker can resolve references to required external libraries (NetCDF and possibly MPI). These tests will point out problems with the user environment in a way that is much easier to understand than looking at the output from a failed build of CAM. We strongly recommend that the first time CAM is built on any new machine, configure should be invoked to execute these tests (see the -test option). 2.1.1 Options to configure All configuration options can be specified in the following ways, listed in order of decreasing precedence: · by invoking configure in interactive prompting mode (enabled with the -i option), · by setting specific options on the command-line, · by a default configuration cache file (specified using the -defaults option). At the next level of precedence a few options can be specified by setting environment variables. And finally, at the lowest precedence, many options have hard-coded defaults. Most of these are located in the file config cache defaults.xml in the configuration script directory. A few that depend on previous settings are hard-coded in configure (a perl script). The hard-coded defaults will produce the standard production configuration of CAM. The interactive prompting mode has two levels: basic and expert. The basic mode, which is enabled by the -i option, asks the user all questions required to configure CAM, assuming that the model is built entirely from code that is contained in the distribution. The expert mode, which is enabled by setting the -x option in addition to -i, allows the user to specify that various pieces of code required to build CAM may come from directories outside the distribution. All 8
the flexibility available in the expert interactive mode is also available from the specific options set on the command-line or from a user specified cache file. The configure script allows the user to specify compile time options such as model resolution, dynamical core type, additional compiler flags, and many other aspects. The user can type configure --help for a complete list of available options. The following options may all be specified with either one or two leading dashes, e.g., -help or --help. Options that can be expressed as single letter switches may not be clumped, e.g., -i -x may NOT be expressed as -ix. When multiple options are listed separated by a vertical bar (|), either version may be used. Table 2.1: Command line arguments to configure
Option Name -cache file -cam bld dir
Description file specifies the pathname of the output configuration cache file. This file is not used in the build process (i.e., the Makefile does not depend on it), but is used instead to archive a complete description of the configuration of a CAM executable. This file is used by the build-namelist utility for setting default namelist values that depend on the configuration of the CAM executable (e.g., which dynamics package and what resolution are used). dir is the directory where CAM will be built. The configuration build files produced by invoking configure are written to this directory. It will eventually contain all the .o and .mod files produced by the build.
Default config cache.xml directory from which configure is invoked
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Option Name -cam cfg dir -cam exe name -cam exedir dir -cam root dir -cc name -debug
Description dir is the directory that contains the CAM configuration scripts, which includes perl modules as well as various defaults files that are required by configure. It is possible (but not recommended) to move configure to another directory, but then the configuration script directory must be explicitly specified so that configure can find its support files. Normally this directory will be determined by looking at the pathname that is used to invoke configure (assuming that configure has not been moved from the configuration script directory). If configure is not in the configuration script directory, then that directory can be specified either by this option, by setting the environment variable CAM CFGDIR to the configuration script directory, or by setting the environment variable CAM ROOT to the root directory of the CAM distribution assuming that the configuration directory is $CAM ROOT/models/atm/cam/bld. name is the name of the CAM executable file.
Default directory part of the absolute pathname used to invoke configure cam
dir is the directory where the CAM executable will the CAM build di-
be created.
rectory
dir specifies the top level directory of a CAM distribution. This directory must contain the subdirectory models which must contain the subdirectories atm, csm share, ice, and lnd. The CAM root directory can also be specified by setting the environment variable CAM ROOT. name specifies the C compiler. This allows the user to override the default setting in the Makefile (Linux only). The C compiler can also be specified by setting the environment variable USER CC. Enable the compiler debugging options that are specified in the Makefile.
config dir/../../../.. where config dir is the directory containing the configure executable. pgcc if using pgf90, otherwise use cc no debugging
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Option Name -defaults file -dyn name -esmf bld dir -esmf root dir -fc name -fflags string -gmake name
Description file specifies the pathname of a configuration cache file that will used to provide default values, e.g. a config cache.xml from a previous invocation of configure. Note that by default the current configuration will be written to a file named config cache.xml, so the user should avoid running configure in the same directory in which the defaults file is located. Alternatively the output cache file can be renamed by using the -cache option. name specifies the dynamics package to be used when running CAM. The valid options are eul (Eulerian spectral dynamics), sld (semiLagrangian spectral dynamics), and fv (finitevolume dynamics). dir is the top level directory where the ESMF library will be built. It will contain the directories mod, lib/libg and/or lib/libO which each contain subdirectories that contain machine architecture specific files. dir is the top level directory for the ESMF distribution. This directory contains the main makefile for the ESMF library. The ESMF root directory can also be specified by setting the environment variable ESMF ROOT. Note that the ESMF library is supplied as part of the CAM distribution, and by default the supplied library is built and used by CAM. This option allows for a custom build of CAM that builds an ESMF library using source code from outside the CAM distribution. name specifies the Fortran compiler. This allows the user to override the default setting in the Makefile. The Fortran compiler can also be specified by setting the environment variable USER FC. The Fortran compiler options specified by string will be appended to the default setting of FFLAGS in the Makefile. If string contains any whitespace it must be quoted. Name of the GNU make program on your system. Supply the absolute pathname if the program is not in your path (or fix your path). This is only needed if testing will be done (see -test).
Default none eul cam bld/esmf, where cam bld is the build directory for CAM. $CAM ROOT/ models/utils/esmf, where cam root is the root directory of the CAM distribution. OS dependent The names 'gmake', 'gnumake', and 'make' are checked in order.
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Option Name -h | -help -i | -interactive -mpi inc dir -mpi lib dir -nadv num
Description Print usage to STDOUT.
Default
Turns on the basic interactive prompting mode. In the basic prompt mode only questions required to obtain a standard configuration of CAM will be asked. To allow configurations which require code from outside the CAM distribution, an expert prompt mode can be enabled by additionally specifying the -x option. In either mode a default value for each setting will be determined based on, in order of decreasing precedence, the specific command-line option for that setting, a user specified default configuration cache file, an environment variable, or a hard-coded default. This default value may then be accepted by entering "return", or overridden by the user. Values are checked when possible for legality and consistency. dir is the directory that contains the MPI library include files. Only SPMD versions of CAM require MPI. The MPI include directory can also be specified by setting the environment variable INC MPI. dir is the directory that contains the MPI library. Only SPMD versions of CAM require MPI. The MPI library directory can also be specified by setting the environment variable LIB MPI. num is the number of advected constituents. This value must be at least 3 because water vapor, cloud liquid, and cloud ice are always advected constituents.
/usr/local/include except on IBM systems. The IBM Fortran compilers mpxlf90 and mpxlf90 r have the MPI include file location built in. /usr/local/lib except on IBM systems. The IBM Fortran compilers mpxlf90 and mpxlf90 r have the MPI library location built in. 3
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Option Name -nc inc dir -nc lib dir -nlat num -nlev num -nlon num -nnadv num -ocn name -pergro
Description dir is the directory that contains the NetCDF library include files. All configurations of CAM require NetCDF. The NetCDF include directory can also be specified by setting the environment variable INC NETCDF. dir is the directory that contains the NetCDF library. All configurations of CAM require NetCDF. The NetCDF library directory can also be specified by setting the environment variable LIB NETCDF. num is the number of model grid latitudes. This option is only recognized when the -res option is set to custom.
Default /usr/local/include /usr/local/lib 64
num is the number of model vertical layers.
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num is the number of distinct model grid longi- 128 tudes. This option is only recognized when the -res option is set to custom. num is the number of non-advected constituents. 0 The default value is 0. Select an ocean model. name can be either dom, dom which indicates the data ocean model, or som, which indicates the slab ocean model. Configure CAM to enable perturbation growth experiments. Note that this option disables parts of the CAM code that have been found to produce rapid growth of roundoff size perturbations.
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Option Name -res name -s | -silent -[no]smp -[no]spmd -[no]test
Description name specifies the horizontal resolution. For spectral dynamics the horizonal grid is Gaussian and is specified as nlat x nlon where nlat is the number of Gaussian latitudes and nlon is the number of distinct longitudes. For finite-volume dynamics the meridional grid is equally spaced and includes the pole points. It is specified as dlatxdlon where dlat is the latitude cell size and dlon is the longitude cell size, both in degrees. All of the valid resolutions are listed in the resolution parameters.xml file in the configuration script directory. Commonly used resolutions include 48x96, 64x128, and 128x256 for the spectral dycores, and 2x2.5 for the FV dycore. To configure CAM for a resolution that is not in the resolution parameters.xml file the value of -res must be set to custom. NOTE: some resolutions recognized by this option are for development purposes only. The recognition of a resolution by this option does NOT imply the existence of a validated control run. Turns off all output to STDOUT. Fatal error messages will still be issued to STDERR.
Default 64x128
-smp enables an SMP configuration of CAM (via SMP is enabled by
openMP). -nosmp disables an SMP configuration default only on IBM
of CAM.
and SGI systems.
-spmd enables an SPMD configuration of CAM SPMD is enabled
(via MPI). -nospmd disables an SPMD configura- by default only on
tion of CAM.
IBM systems.
-test enables testing the Fortran compiler and external libraries and -notest disables testing. The tests are: 1. Check that the Fortran compiler will successfully build a "hello world" program that uses Fortran 90 module syntax. 2. Check that the Fortran compiler will successfully build a test program that contains an external reference to a NetCDF library function. 3. Check that the Fortran compiler will successfully build a test program that contains an external reference to an MPI library function, if SPMD is enabled.
testing off except in interactive prompting mode
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Option Name
Description
num is the spectral resolution parameter that
-trk num
specifies the highest degree of the associated Legendre polynomials. This option is only recognized
when the -res option is set to custom.
num is the spectral resolution parameter that
-trm num
specifies the maximum Fourier wavenumber. This option is only recognized when the -res option is
set to custom.
num is the spectral resolution parameter that
-trn num
specifies the highest degree of the Legendre polynomials for m=0. This option is only recognized
when the -res option is set to custom.
dir1[,dir2[,dir3[...]]] specifies the directories con-
taining user source code. These directories will
-usr src
be placed, in the order in which they are speci-
dir1[,dir2[...]] fied, at the beginning of the Filepath file. The
Filepath file is used by the CAM Makefile to de-
termine which source files will be compiled. The
list of source files is comprised of all files with
.F90, .F, or .c extensions in each directory listed in
Filepath plus the current directory. The Filepath
file is also used by the CAM Makefile to determine
which directories will be searched when looking
for a source file that can be used to build an ob-
ject file. The search begins in the current direc-
tory, and then proceeds to the directories in the
Filepath file, in the order in which they are spec-
ified. The first file found will be the one used by
make to create the object file.
num specifies the verbosity level of the output to
-v num
STDOUT. Level 1 echos only the names of the files produced by configure. Level 2 adds echoing
of the configuration specifications associated with
a standard build of CAM. Level 3 adds echoing
of the specifications associated with an "expert"
build of CAM.
Echo the CVS tag name that was used to check
-version
out the CAM distribution, then exit. If no tag was used for the check-out then the string N ame
will be echoed.
Default 42 42 42 none 1
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Option Name -x
Description
Default
Turns on the "expert" interactive mode. See the
-i option for more details.
2.1.2 Environment variables used by configure The environment variables recognized by configure are presented in Table 2.2. Table 2.2: Environment variables used by configure
Variable Name CAM ROOT CAM CFGDIR ESMF ROOT
Description The root directory of the CAM distribution. The directory containing the configuration scripts is $CAM ROOT/models/atm/cam/bld. The directory that contains the CAM configuration scripts. This is provided only for the special case that the configuration scripts are taken from a directory outside of the CAM distribution. Root directory to the ESMF source code.
INC NETCDF
Directory containing the NetCDF include files.
LIB NETCDF
Directory containing the NetCDF library.
INC MPI
Directory containing the MPI include files. This is only required when CAM is built with SPMD enabled.
LIB MPI
Directory containing the MPI library. This is only required when CAM is built with SPMD enabled.
USER FC
User specified Fortran compiler. Overrides Makefile default.
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Variable Name USER CC
Description User specified C compiler. Overrides Makefile default. Currently only recognized on linux systems.
2.2 The build-namelist utility The build-namelist utility builds namelists which specify run-time details for CAM and CLM. These are written to a single file (by default, the file namelist in the directory from which build-namelist is invoked). The only required input for build-namelist is a configuration cache file produced by a previous invocation of configure (./config cache.xml by default). build-namelist looks at this file to determine the features of the CAM executable, such as the dynamical core and horizontal resolution, that affect the default specifications for namelist variables. The default values themselves are specified in the files DefaultCAMEXPNamelist.xml and DefaultCLMEXPNamelist.xml in the CAM configuration script directory. The user can specify namelist values that are not set by default, or can override the values that are set by default, in a number of ways. The method with highest precedence is to use the specific command-line options indicated in Table 2.3. The next highest precedence is given to any values set on the command-line using the -namelist option. Finally, at the lowest precedence, the default values are used. There is also an interactive prompting option (-i) which allows the user to view the namelist produced by the default and command-line settings, and make final changes.
2.2.1 Options to build-namelist
To get a list of all available options, type build-namelist --help. Available options are also provided here in Table 2.3. All options may be specified with either one or two leading dashes, e.g., -help or --help. When multiple options are listed separated by a vertical bar (|), either version may be used.
Table 2.3: Command line arguments to build-namelist
Option Name
Description
Default
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Option Name -cam cfg dir -case name -config file -csmdata dir -h | -help
Description dir is the directory that contains the CAM configuration scripts, which includes perl modules as well as various defaults files that are required by build-namelist. It is possible (but not recommended) to move build-namelist to another directory, but then the configuration script directory must be explicitly specified so that build-namelist can find its support files. Normally this directory will be determined by looking at the pathname that is used to invoke build-namelist (assuming that build-namelist has not been moved from the configuration script directory). If buildnamelist is not in the configuration script directory, then that directory can be specified either by this option, by setting the environment variable CAM CFGDIR to the configuration script directory, or by setting the environment variable CAM ROOT to the root directory of the CAM distribution assuming that the configuration directory is $CAM ROOT/models/atm/cam/bld. name is the case identifier for the CAM run (up to 32 characters). This value is used to set the caseid variable in the CAM namelist.
Default directory part of the absolute pathname used to invoke build-namelist camrun
file is a configuration cache file produced by the config cache.xml configure script. build-namelist obtains the configuration of the CAM executable from this file.
dir is the root directory for the default initial and boundary datasets supplied with the CAM distribution. This directory can also be specified by setting the CSMDATA environment variable. It is assumed that the root directory will contain the subdirectories atm/cam2 for CAM datasets and lnd/clm2 for CLM datasets. Print usage to STDOUT.
/fs/cgd/csm/ inputdata. This value is set in the files DefaultCAMEXPNamelist.xml and DefaultCLMEXPNamelist.xml in the CAM configuration script directory.
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Option Name -i | -interactive -infile file -namelist namelist -o file -runtype name -s | -silent -test -v num
Description
Default
Turns on interactive prompting to modify a
namelist.
file is a namelist file to read values from. All values read from this file will appear in the output namelist unless they are overridden by other values having higher precedence. namelist is a string that contains namelist settings using valid namelist syntax, e.g., -namelist "&camexp nelapse=-10, empty htapes=.true. /" Namelist values set on the command-line take precedence over values read from a file specified with the -infile option. file is the filename of the output namelist.
none none namelist
name specifies the type of simulation. Valid values initial are initial, restart, or branch. Turns off all output to STDOUT. Fatal error messages will still be issued to STDERR. Enable checking that initial and boundary no checking datasets exist on local filesystem. num specifies the verbosity level of the output to 1 STDOUT. The default (1) echos only the name of the file produced by build-namelist. Level 2 adds echoing of the results from the -test option, and level 3 adds echoing of the default values read from the files in the CAM configuration script directory.
2.2.2 Environment variables used by build-namelist The environment variables recognized by build-namelist are presented in Table 2.4.
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Table 2.4: Environment variables used by build-namelist
Variable Name CSMDATA CAM ROOT
Description The root directory for the default initial and boundary datasets supplied with the CAM distribution. It is assumed that the root directory will contain the subdirectories atm/cam2 for CAM datasets and lnd/clm2 for CLM datasets. The root directory of the CAM distribution. The directory containing the configuration scripts is $CAM ROOT/models/atm/cam/bld.
CAM CFGDIR
The directory that contains the CAM configuration scripts. This is provided only for the special case that the configuration scripts are taken from a directory outside of the CAM distribution.
2.3 Use Cases This section provides a few examples of using configure and build-namelist to set up a variety of model runs. These examples were chosen to illustrate many of the configuration and namelist options described above and in the section named CAM Namelist Variables (B). They do not discuss the intricacies of running CAM 3.0 on its various supported platforms; a discussion of that topic may be found in the section named Sample Run Scripts (2.4). The following use cases have been tested on a linux PC using the Portland Group compiler (pfg90). These examples assume a stand-alone configuration of CAM 3.0. Furthermore, it is assumed that the root directory for the CAM 3.0 dataset distribution is /data. (The root directory contains the subdirectories atm and lnd.) The examples in this section all assume that the CAM configuration script directory is located in the standard place within the CAM distribution. It is also assumed that the CAM configuration directory is not in the user's PATH environment variable. For this reason the configure script must be invoked using an absolute pathname. The script attempts to use the pathname that it was invoked with to determine the configuration script directory. If this is successful then configure can determine the CAM root directory without the user needing to set the CAM ROOT environment variable. 2.3.1 Configuring and running the default CAM executable The following interactive C shell session builds a default production version of CAM. The shell variable tmpdir is set to a working directory on the user's system, and camcfg is set to the CAM configuration directory ($CAM ROOT/models/atm/cam/bld). The following output is from a linux system, but will appear similar on other machines. % cd $tmpdir % $camcfg/configure -test 20
creating /big/data/temp/Filepath creating /big/data/temp/params.h creating /big/data/temp/misc.h creating /big/data/temp/preproc.h creating /big/data/temp/Makefile creating /big/data/temp/config_cache.xml Looking for a valid GNU make... using gmake Testing for Fortran 90 compatible compiler... using pgf90 Testing NetCDF library... ok configure done. % gmake -j2 >&! make.out % setenv CSMDATA /data % $camcfg/build-namelist -test Write out namelist to: namelist % ./cam < namelist >&! output.txt
We started by changing into the directory in which the CAM executable will be built. All
the files produced by configure except for the cache file are required to be in the CAM build
directory, so it is generally easiest to be in that directory when configure is invoked. This
example was carried out on a linux machine. We recommend using the -test option the first
time CAM is built on any machine. This will check that the environment is properly set up so
that the Fortran compiler works and can successfully link to the NetCDF and MPI (if SPMD
enabled) libraries. The testing tells us that gmake is a GNU Make on this machine, that the
Fortran compiler is pgf90, and that the compiler can successfully reference the NetCDF library.
We then issued the gmake command with a -j2 option, which tells gmake to use 2 processors
for the build. Output from the make, including the messages issued to STDERR, are redirected
to the file make.out. In the event of an error during the build, the make.out file will contain
the command that was issued by gmake that resulted in the error.
Next we set the environment variable CSMDATA to point to the root of the input data
distribution (where we unpacked the intput dataset tar files).
Next we issued the build-namelist command. The first time a namelist for a particular
CAM configuration is produced, we recommend using the -test option which checks whether
the initial and boundary datasets exist on a local filesystem. If they do not then a warning is
issued to inform the user which datasets must be copied to the directory from which CAM will
be run. The execution of build-namelist with -test produces the following default namelist:
&camexp ABSEMS DATA AEROPTICS BNDTVAER BNDTVDMS BNDTVGHG
= '/data/atm/cam2/rad/abs_ems_factors_fastvx.c030508.nc' = '/data/atm/cam2/rad/AerosolOptics_c040105.nc' = '/data/atm/cam2/rad/AerosolMass_V_64x128_clim_c031022.nc' = '/data/atm/cam2/rad/DMS_emissions_64x128_c030722.nc' = '/data/atm/cam2/ggas/ghg_1870_2100_c040122.nc'
bndtvo bndtvoxid bndtvs bndtvscon bndtvsox bndtvvolc
= '/data/atm/cam2/ozone/pcmdio3.r8.64x1_L60_clim_c970515.nc' = '/data/atm/cam2/rad/oxid_3d_64x128_L26_c030722.nc' = '/data/atm/cam2/sst/sst_HadOIBl_bc_64x128_clim_c020411.nc' = '/data/atm/cam2/rad/scon_1870_2100_c040122.nc' = '/data/atm/cam2/rad/SOx_emissions_64x128_L2_c030722.nc' = '/data/atm/cam2/rad/VolcanicMass_1870-1999_64x1_L18_c040115.nc'
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caseid iyear_ad ncdata nelapse nsrest / &clmexp finidat fpftcon fsurdat /
= 'camrun' = 1950 = '/data/atm/cam2/inic/gaus/cami_0000-09-01_64x128_L26_c030918.nc' = -1 =0 = '/data/lnd/clm2/inidata_2.1/cam/clmi_0000-09-01_64x128_T42_USGS_c030609.nc' = '/data/lnd/clm2/pftdata/pft-physiology' = '/data/lnd/clm2/srfdata/cam/clms_64x128_USGS_c030605.nc'
build-namelist used the configuration cache file (config cache.xml ) that was produced by configure to determine the dynamics package, land model, and resolution of the CAM executable. This information was used to choose the default initial and boundary datasets. The default run type is an initial run (nsrest=0), the run length is 1 day beyond the date of the initial conditions (nelapse=-1), and the valid year for the calculated orbital parameters is 1950 (iyear ad=1950). The absence of warnings from build-namelist indicates that all the initial and boundary datasets were found on the local filesystem. Finally, we execute the cam executable and tell it to read its standard input from the namelist file. On systems that support running in SPMD mode this command line will be more complicated, and will typically involve a poe (on NCAR's IBM AIX machines) or a mpirun (on linux clusters) command. Please see the section named Sample Run Scripts (2.4) for details. When the model is done executing, the directory should contain the files:
camrun.cam2.r.0000-09-02-00000 camrun.cam2.rh0.0000-09-02-00000 camrun.clm2.r.0000-09-02-00000
These are, respectively, a CAM master restart file, a CAM history buffer restart file, and a CLM restart file. There is no regular CAM history file because by default these are output monthly, and this was only a one day run.
2.3.2 Using the Slab Ocean Model (SOM) The default prescribed-SST, prescribed-ice configuration of the standalone CAM model can be swapped out and replaced with a mixed-layer slab ocean model (SOM). Mixed layer temperature is the prognostic variable output from SOM. The thermodynamic ice model configured with SOM is the same as in CAM when run in prescribed-ice mode, with two additions. First, ice fraction is predicted rather than read from a boundary dataset. Second, ice thickness is also predicted, rather than fixed at 2 meters in the northern hemisphere and 1 meter in the southern hemisphere. Since SOM-configured CAM is run on the same horizontal grid as CAM, the CCSM flux coupler is not used. Before a SOM run can be initiated, a boundary dataset must be built which contains SOMspecific information. Required steps are: 1) Define annually averaged mixed layer depths at the target horizontal resolution. Instructions for this procedure are contained in subdirectory models/atm/cam/tools/definemld of the CAM source tree. From this directory, an example sequence of commands to define mixed layer depths (after running gmake) might be:
22
./definemld1x1 -m mldfile.nc -v ./definemldbdy -s 10 -v -i mldfile.nc -o sst.nc The first command creates mixed layer depth information at a horizontal resolution of 1 degree by 1 degree from ASCII input files, which are provided in the directory. The next command averages these data to the horizontal grid defined by a template file (sst.nc in the example). The mixed layer depths are written to the template file. A good choice for a template file is an existing prescribed ice/SST dataset at the desired resolution. 2) Define surface flux balance information from a control run which was done with prescribed ice and SSTs. Detailed build and execute instructions are contained in subdirectory models/atm/cam/tools/defineqflux. After building the executable, the command to construct the final boundary dataset looks something like: ./defineqflux -f firstfile_fromcontrolrun -l lastfile_fromcontrolrun -s sst.nc -v The sequence of monthly history files from a control run is defined by the arguments to "-f" and "-l". All monthly data defined by these time boundaries must be in the working directory before running defineqflux. Output flux balance variables are written to the output file defined by the "-s" argument. Both the control run and the output file must be at the same horizontal resolution. Example boundary dataset sst.nc is now ready for use by a SOM-enabled CAM. To configure CAM to be run in SOM mode, Filepath must be modified to include som instead of dom. Secondly, cpp token COUP SOM must be defined in the file misc.h. Both of these tasks can be accomplished by running configure with "-ocn som". 3) Once CAM has been built with SOM as the underlying ocean model, namelist variable "bndtvs" needs to point to the SOM-specific boundary dataset described above. Since ocean surface temperature (i.e. mixed layer temperature) is a prognostic variable when SOM is enabled, model equilibration times are generally much longer than when SSTs and ice fraction are prescribed. Forty years or more of integration time may be needed for the model to reach a quasi-equilibrium state. Annually averaged mixed-layer depths (described above) are capped at 200 meters to prevent even longer equilibration times. 2.4 Sample Run Scripts Sample run scripts are provided that illustrate how to use configure and build-namelist to set up a production run on an IBM-SP, an SGI Origin, or a PC-Linux platform. Before we present the example run scripts, we first discuss details of the multitasking strategy employed in CAM 3.0. Both shared-memory multitasking (using OpenMP) and distributed memory (using MPI) multitasking is allowed. Hybrid-mode enables both shared-memory (for CPU's within a node) and distributed-memory (between nodes) multitasking. Shared-memory multitasking requires the run-time specification of the number of processors to use (by setting the environment variable $OMP NUM THREADS). Distributed memory 23
multitasking involves the use of the MPI message-passing programming paradigm. The messagepassing code has been validated on IBM SP3, SGI (IRIX), and Linux platforms. Different implementations of MPI handle the settings of the number of tasks in different ways. The sample run scripts are contained in the directory $CAM ROOT/models/atm/cam/bld/ in the files run-ibm.csh, run-sgi.csh, and run-pc.csh. They are set up to build and run the default CAM configuration, i.e., Eulerian dynamics at T42 spectral resolution (about 2.8 degree grid spacing) with 26 vertical levels, CLM2 land model, and CSIM4 ice model. The following list describes the features of the scripts, and how to customize them. Root directory of CAM source distribution The shell variable CAM ROOT must be set to the root directory of the CAM distribution. This variable is used to set the directory of the configuration utilities which is assumed to be $CAM ROOT/models/atm/cam/bld. Root directory of CAM dataset distribution The environment variable CSMDATA must be set to the root directory of the CAM dataset distribution. The value in the run scripts is appropriate for runs at NCAR on machines that mount the /fs filesystem. CSMDATA is used by the build-namelist utility to specify the locations of initial and boundary datasets used by CAM and CLM2. CAM work directory The work directory is specified by the shell variable wrkdir. The defaults are appropriate for NCAR machines and are large capacity temporary filesystems. The scripts assume that the CAM build and run directories will be subdirectories of the work directory. CAM run directory The run directory is specified by the shell variable rundir. By default this is set to a subdirectory of the work directory which has the same name as the run's case name (which is a required namelist input). The script will create this directory if it doesn't exist, and will exit if an error is encountered trying to create the directory. CAM build directory The build directory is specified by the shell variable blddir. By default this is set to the bld subdirectory of the run directory. The script will create this directory if it doesn't exist, and will exit if an error is encountered trying to create the directory. Configuration of CAM The configuration of CAM is done by calling the configure utility. The default configuration may be changed by supplying the appropriate arguments to configure. Building CAM The script will check for an executable named cam in the build directory. If no executable exists then the script changes to the build directory and issues the configure and gmake commands. If the GNU make command on your system is not called "gmake", or if it is not in your PATH, then the gmake in the script will need to be changed to the appropriate name. gmake is invoked with the -jn option where n is the number of simultaneous compilation commands issued. This number should not be larger than the number of processors available for the build. 24
2.4.1 Use of C preprocessor tokens cpp directives of the form #include, #if defined, etc., are used to enhance portability, and allow for the implementation of distinct blocks of platform-specific code within a single file. Header files, such as misc.h, are included with #include statements within the source code. When gmake is invoked, the C preprocessor includes or excludes blocks of code depending on which cpp tokens have been defined. cpp directives are also used to perform textual substitution for resolution-specific parameters in the code. The format of these cpp tokens follows standard cpp protocol in that they are all uppercase versions of the Fortran variables, which they define. Thus, a code statement like parameter(plat = PLAT) will result in the following processed line (for standard T42 resolution). parameter(plat = 64) 2.4.2 Details of the gmake procedure gmake invokes the utility mkSrcfiles to generate a list of source files (written to the file Srcfiles) using each directory listed in Filepath. gmake then invokes the utility mkDepends to create a dependency file (written to the file Depends) in the CAM build directory. If a file listed as a dependency does not exist in the CAM build directory, gmake searches the directories contained in Filepath, in the order given, for a file with that name. The first file found satisfies the dependency. If user-modified code is to be introduced, Filepath should contain, as the first entry (or entries), the directory containing the user code. User code directories are specified with the -usr src option to configure. A parallel gmake is achieved in the build scripts by using gmake with the -j option, which specifies the number of jobs (commands) to run simultaneously. The output from the build is written to the file MAKE.out in the build directory. If a build fails this is the first place to look for information. Rebuilding CAM The scripts are set up to not rebuild CAM if an executable already exists. To use the script in the situation where a rebuild of only the code (and its dependencies) that has been modified is desired, the script must be edited by commenting out the conditional statement that tests for the existence of a cam executable. Also, the configure command must be commented out since rerunning it will update the configuration files (e.g., misc.h) that all the source files depend on, and hence will result in a complete rebuild. Creating the namelist The script will change into the build directory and issue the build-namelist command. The reason for the change to the build directory is that that is the location of the config cache.xml file produced by configure which is used by build-namelist. The namelist is created in a file called namelist which is written to the run directory. The case name, run type, and elapsed length of run are set by assigning values to the shell variables case, runtype, and nelapse respectively. Other changes to the namelist may be made by modifying the -namelist argument of the build-namelist command. 25
Before discussing the namelist variables, a brief summary is given of the types of model runs. An initial run starts the model from an initial conditions dataset. As the model executes, history datasets, restart datasets and initial condition datasets are periodically written. (see "Model Output Datasets") and "Model generated initial condition dataset files" for more details). In addition to initial simulations, there are two types of continuation runs: restart and branch. A restart run is an exact continuation of a previous simulation from its point of termination. Namelist variables other than NESTEP, NELAPSE, and NSREST should never be modified for restart runs. A branch run, on the other hand, is a new case that uses restart data from a previous simulation to begin the integration. Since a branch run is a new case, the length of the history interval and the output history fields do not have to be the same as in the control simulation. For example, the branching option can be used to output selected fields more frequently than was the case in the control run. Only history file namelist options should be modified for branch runs. If the user desires to modify other options, such as physics control variables, a new initial run should be done using initial datasets generated by the control run. The user should also note that any namelist variable that can be used as a part or all of a UNIX pathname (e.g. CASEID,NREVSN,..) should only contain characters that are acceptable in UNIX path names. The set of CLMEXP namelist variables that must be specified depends on whether or not a CLM 3.0 surface dataset is available at the desired model resolution. If such a dataset exists, then build-namelist will provide the minimum set CLMEXP of namelist variables that must be specified: · FPFTCON Specifying the filepath to the plant function types dataset. · FSURDAT Specifying the filepath to the CLM surface dataset. If a CLM surface dataset is to be created at run time, then the build-namelist will attempt to provide the following CLM namelist variables: · FPFTCON Specifying the filepath to the plant function types dataset. · MKSRF FVEGTYP Specifying the file to the high resolution vegetation type dataset. · MKSRF FSOITEX Specifying the file to the high resolution soil texture dataset. · MKSRF FSOICOL Specifying the file to the high resolution soil color dataset. · MKSRF FLANWAT Specifying the file to the high resolution lake water dataset. · MKSRF FURBAN Specifying the file to the high resolution urban area dataset. · MKSRF FGLACIER Specifying the file to the high resolution glacier dataset. · MKSRF FLAI Specifying the file to the high resolution leaf area index dataset. The above datasets define the time invariant surface information, but do not provide initial condition information for the land model. If initial conditions at the specified resolution are available, they will provided by build-namelist via the namelist variable "FINIDAT". · FINIDAT Specifying the filepath to initial condition dataset. NOTE: When the user provides FSURDAT or FINIDAT datasets to the model the surface land mask and orography MUST agree with the land mask and 26
orography of the atmospheric model initial conditions dataset (ncdata). Furthermore, the land informaton must agree between the FINIDAT and FSURDAT datasets as well. Running on an IBM The default parallelization on the IBM is hybrid MPI/OpenMP. The script is set up for NCAR's machine which has 4 processor nodes. One MPI process (task) is assigned to each node and by default the number of threads is set to the number of processors on each node. The number of nodes is set by either the #@node loadleveler variable if running in batch mode, or by the MP NODES environment variable if running interactively. For the spectral dynamical cores the number of MPI processes is restricted to being a power of 2. Changing the number of MPI processes per node is done by setting either the #@tasks per node loadleveler variable if running in batch mode, or by the MP TASKS PER NODE environment variable if running interactively. If more than 1 MPI process is assigned to a node then the number of threads for each task should be reduced so that the number of MPI processes times the number of threads per process does not exceed the processor count on the node. The number of threads per process can be set by changing the value of the XLSMPOPTS environment variable. For example the number of threads is set to 2 with the string "stack=86000000:parthds=2". Running on an SGI The default parallelization on the SGI is pure OpenMP. The script is setup to use the default number of threads which is set to the number of processors on the machine, or to the number available in the queue if running in batch mode. This number can be reduced by uncommenting the setenv command for OMP NUM THREADS environment variable and setting it to the desired number. The script also uses some module commands which set up the system environment for NCAR machines. These commands may need to be commented out or modified on non-NCAR platforms. Running on a PC The PC run script is set up to illustrate a pure OpenMP run. Since the default shared memory processing for the PC in the configure utility is none, the -smp option must be supplied to build CAM for an OpenMP run. The number of processes is set by the shell variable nthreads. The PC script does not have a batch queue submission capability. Running batch jobs The IBM and SGI scripts both contain lines that control batch queue submission. On the IBM the loadleveler variable #@class must be set to a valid queue name, and the run script submitted using the llsubmit command. On the SGI the -q option to the qsub command must be set to a valid queue name, and the run script is submitted using the qsub command. 2.5 Model Input Datasets CAM2.0.2 is a combination of atmosphere, land, ocean and sea-ice components. In what follows we discuss the input datasets required by each of these components. CSMDATA refers to the root directory where the distribution datasets have been untarred by the user. 27
2.5.1 Atmosphere Component Datasets Input datasets needed for the atmospheric component provide initial state data, ozone boundary data and water vapor absorptivity/emissivity data. Only the ozone dataset contains time-variant input data which is based on a 365 day year with no leap years. All initial and boundary datasets are in NetCDF format. In general, input dataset names follow the convention: Where · Simulation date = The specific date that the given dataset is valid for. In the case of initial condition datasets this is typically given in YYYY-MM-DD form. Datasets that are valid over a span of dates typically list the year range. · Resolution = Number of latitudes by the number of longitudes for the grid being used (i.e. 64x128, 32x64 etcetera). · Spectral truncation = For Spectral dynamical cores (eul or sld) the spectral truncation applied to the dataset (T42, T63 etcera). This is only given if the dataset in question has had spectral truncation applied to it. · Vertical levels = Number of vertical levels (L26, L18 etc.) · Creation date = The date the file was created in cYYMMDD format. Initial Conditions Dataset The initial conditions dataset is specified by namelist variable NCDATA. This dataset contains initial values of the prognostic variables U, V, T, Q, PS, TSICE, SNOWHICE and TS1 through TS4, the surface geo-potential field PHIS, the grid-box land fraction LANDFRAC, the land ocean transition mask LANDM, and the standard deviation of geo-potential height SGH. When running flux-coupled the fields: TSICE, SNOWHICE, LANDFRAC and TS1 through TS4 are not included on the dataset. Required initial fields are outlined in 2.5. At times it may be desirable to start the model from a more exact state of the atmosphere, with some of the fast processes (spin-up time < 1 day) also represented on the initial conditions file. Table 2.6 lists optional fields which the model will read if they exist on the file. Fields which don't exist will be set to arbitrary values as indicated in the table: By default, the model periodically writes an instantaneous initial conditions file containing all the fields in Table 2.5 and Table 2.6 for possible use as initial datasets in other runs. The frequency with which these datasets are written is controlled by the namelist variable INITHIST. Finite-volume dynamics uses the same set of prognostic variables as shown above, except that U and V are on a staggered grid and are identified with names US and VS. When running with finite-volume dynamics, the initial dataset must contain US and VS; U and V are Ignored. All Fields are instantaneous values. In addition to the fields listed above, the initial dataset contains information on the model date, the dimensionality of the fields, the spectral truncation, and the latitudes, longitudes, and vertical levels of the data. A T42 (64 latitudes x 128 longitudes grid resolution) 26-level initial dataset is provided with the CAM2.0.2 distribution: CSMDATA/atm/cam2/inic/gaus/cami 0000-09-01 64x128 T42 L26 c020514.nc. Other initial datasets at different model resolutions can also be found in the directories 28
Table 2.5: Atmospheric Component Initial Dataset Fields
Field Name
Variable Name Description
Multi-Level Fields
T
T
Temperature (K)
U
u
Zonal Wind component (m/sec)
V
v
Meridional Wind component (m/sec)
Q
q
Water vapor specific humidity (KgH2O/Kgair)
Single Level Fields
PHIS PS SGH LANDM
s Ps SGH landm
TS
Ts
TSICE
Tice
SNOWHICE LANDFRAC TS1, TS2, TS3, Ts TS4
Surface geo-potential (m2/s2) Surface pressure (Pa) Standard deviation of geo-potential height (m) Land Ocean transition mask: LANDM = 0 indicates ocean, LANDM = 1 indicates land, and 0 < LANDM < 1 indicates a transition region. Surface temperature. CSIM sea-ice model snow/ice surface temperature (not stored on CCSM flux-coupled simulations). Snow depth over ice Land fraction Four CSIM sea-ice subsurface temperature levels (not stored on CCSM flux-coupled simulations) (K)
29
Table 2.6: Optional Atmospheric component initial dataset fields (representing "fast" processes)
Field Name
Variable Name Description
Multi-Level Fields
CLDLIQ CLDICE CLOUD QCWAT TCWAT LCWAT
q(:,:,,ixcldliq,:) q(:,:,,ixcldice,:) cld qcwat Tcwat lcwat
Cloud liquid water mass mixing ratio (Kgliq/Kgair); set to 0. if READTRACE=.false. or field not on file Cloud ice mass mixing ratio (Kgice/Kgair); set to 0. if READTRACE=.false. or field not on file Cloud fraction ; set to 0. if field not on file Specific humidity associated with cloud water routines ; (KgH2O/Kgair); set to Q if field not on file Temperature associated with cloud water routines ; (K); set to T if field not on file Total cloud water amount (liquid + ice) associated with cloud water routines ; (Kgcwat/Kgair); set to "CLDLIQ+CLDICE" if field not on file
Single-Level Fields
PBLH TPERT QPERT TSICERAD TBOT
pblht Tpert qpert Tice rad Tbot
PBL height (m); set to 0. if field not on file Perturbation temperature (eddies in PBL) (K); set to 0. if field not on file Perturbation specific humidity (eddies in PBL) (KGH2O/KGair); set to 0. if field not on file Radiatively equivalent Surface T over seaice (K); set to TSICE if field not on file Lowest model level temperature (K); set to T(:,plev,:) if field not on file
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CSMDATA/atm/cam2/inic/gaus and CSMDATA/atm/cam2/inic/fv Ozone Dataset The ozone boundary dataset contains ozone volume mixing ratios which are constant for a given latitude. This dataset is defined on a pressure grid (unlike the hybrid grid of the model). These values are interpolated to the model vertical levels at each model grid point. The ozone dataset is in NetCDF format and contains the fields PS and OZONE. PS is a constant 1000 mb pressure field needed for interpolation. The ozone dataset is specified by namelist variable BNDTVO. Unlike the initial conditions file, CAM is capable of interpolating the ozone dataset to any vertical and or horizontal resolution so the user need not specify new ozone datasets when changing model resolution. The default ozone dataset provided with the distribution is CSMDATA/atm/cam2/ozone/pcmdio3.r8.64x1 L60 clim c970515.nc. Water vapor absorptivity/emissivity dataset This is a lookup table for water vapor absorption. It is specified by setting the namelist variable, ABSEMS DATA. The default dataset provided with the dataset distribution can be found in CSMDATA/atm/cam2/rad/abs ems factors fastvx.052001.nc. Aerosol Mass dataset [Science description if any goes here]. As of CAM2.0.2.dev40, CAM requires the input aerosol dataset to be resolution-dependent. Memory and startup CPU overheads proved to be a bottleneck in the original implementation. Now horizontal interpolation to the target CAM grid and vertical integrals are done offline. Code and README describing the procedure are in subdirectory cam/tools/interpaerosols of the CAM distribution. CSMDATA/atm/cam2/rad/abs ems factors fastvx.052001.nc. 2.5.2 Ocean Component Datasets CAM 3.0 supports running with either a data ocean model or a prognostic slab ocean model. The data ocean model simply reads and interpolates sea surface temperature (SST) data. Running the data ocean component requires a time-variant SST dataset. The SST dataset must be at the model resolution and is specified by the namelist variable BNDTVS. The standard SST dataset is a climatological dataset containing 12 monthly time samples. The model can also read multi-year SST datasets. If a multi-year SST dataset is used, the namelist variable, SST CYC must be set to .false. (it's default value is .true.). An SST dataset on a (64 X 128) Gaussian grid can be found in CSMDATA/atm/cam2/sst/sst HadOIBl bc 64x128 clim c020411.nc. Other SST datasets, at different model resolutions, can also be found in this directory. The slab ocean model requires that the SST dataset specified by BNDTVS contain two additional fields specifying mixed layer depths and Q-fluxes. Preparation of these special SST datasets for the slab ocean model is described in Section 2.3.2. 31
2.5.3 Sea-Ice Component Datasets The sea-ice component in CAM2.0.2 is a simplified version of the CCSM CSIM4 code. This component requires ice coverage data. The ice coverage data is contained in the same file as the SST data required by the ocean component. For the standard configuration, ice-coverage data is found in CSMDATA/atm/cam2/sst/sst HadOIBl bc 64x128 clim c020411.nc. 2.5.4 Land Component Datasets For a full discussion of CLM2.1 input datasets see the CLM2.1 User's Guide at http://www.cgd.ucar.edu/tss/clm/distribution CLM2.1 always requires a dataset providing plant functional type physiological constants. This dataset is specified via the CLM2.1 namelist variable FPFTCON. A time-invariant CLM surface dataset will be generated at run time if the CLM namelist variable FSURDAT is set to blank. If this is the case, additional settings must be provided for MKSRF FGLACIER, MKSRF FLAI, MKSRF FLANWAT, MKSRF FSOICOL, MKSRF FSOITEX, MKSRF FURBAN, MKSRF FVEGTYP. If a surface dataset at the model resolution already exists, then FSURDAT should be set appropriately. The default land surface dataset provided with the distribution is CSMDATA/lnd/cam/srfdata/cam/clms 64x128 c020514.nc. Other provided surface datasets at other model resolutions can also be found in this directory. CLM2.1 initial conditions will be generated at run time if the CLM2.1 namelist variable FINIDAT is blank (the default setting). It is important to note that due to the differences in data structures, CLM2.1 initial datasets are not in the same form as CLM2.0 initial datasets. The directory models/lnd/clm2/tools/convert inic contains routines needed to perform the conversion of CLM2.0 initial datasets to CLM2.1 form. The README file in that directory contains necessary information to build and utilize the conversion tool. If spun up values exist for a model run, then FINIDAT should be correspondingly set. The default initial dataset provided with the distribution is: CSMDATA/lnd/clm2/inidat 2.1/cam/clmi 0000-09-01 64x128 T42 c021125.nc. This initial dataset should only be used in conjunction with the default CLM2.1 surface dataset given above. 2.6 Troubleshooting Guide This section presents information which should help with some common problems users encounter when running the CAM. Supported Platforms for CAM 3.0 CAM 3.0 is ported to and supported on the following platforms: · IBM-SP · SGI-Origin · Linux-PC with the Portland group fortran compiler and GNU C compiler. · Linux-PC with the Portland group fortran compiler and Portland Group C compiler. 32
· Linux-PC with the Lahey fortran compiler. Known problems · Potential problem on all platforms getting environment variables when running with distributed memory parallelism (SPMD mode). The model code requires that certain environment variables be available. When running in "SPMD mode" each processing task has to establish these values. Some machines have trouble when processing slaves try to get environment variables. For example, using the UNIX shell "bash" on a Linux platform with the Lahey compiler ­ the model fails since the slave processes are unable to obtain the environment variables. This problem can be related to the UNIX shell that the user is using. Running on Linux with the Lahey compiler and the "tcsh" shell doesn't cause the same problem that running "bash" does. Users are cautioned that other combinations of UNIX shells and platforms may result in this same problem. · Problem compiling "history.F90" on IBM-SP with DEBUG mode and SPMD on. The model has undergone extensive testing on IBM platforms both at NCAR and at several other institutions. One problem discovered is a problem compiling the "history.F90" module when using the more extensive "DEBUG mode" compiler options (this mode is enabled by setting the environment variable DEBUG to "TRUE") and with the SPMD distributed memory configuration. The compiler will sometimes abort with the error "INTERNAL COMPILER ERROR". This problem is due to a problem with the IBM FORTRAN-90 compiler, and has been reported to IBM. In many cases this problem is inconsistent, so recompiling will sometimes (not always) work. As a work around the user could also compile "history.F90" without the DEBUG option on. This problem was reported to IBM and they have fixed the problem in newer versions of the compiler (or with the appropriate "E-fixes" applied to older compilers). · Problem building ESMF library with some versions of gmake. Certain versions of gmake have been shown to have trouble with date-stamps. The Earth System Modeling Framework (ESMF) library has trouble with these versions and will not build. The version of gmake with the fix is 3.79.1, the bug was introduced somewhere between 3.78.1 and 3.79. So to fix the problem you merely need to update to a newer version. General The first step in troubleshooting a failed model run is to check the basics. Look at the logs for error messages. Make sure the model executable is up to date with any source code changes. Rebuild the model cleanly (i.e. issue a "gmake clean" before rerunning the script) if you are unsure of the state of any code. Ask yourself what has changed since the last successful run. Other times CAM may fail for no obvious reason or perhaps the error message returned is cryptic or misleading. It has been our experience that the majority of these types of symptoms can be attributed to an incorrect allocation of hardware and/or software resources (e.g. the user sets the value of $OMP NUM THREADS to a value inconsistent with the number of physical CPUs per node). Most often an incorrect setting for the per-thread stack size will cause the 33
model to fail with a segmentation fault, allocation error, or stack pointer error. Usually the default setting for this resource is too low and must be adjusted by setting the appropriate environment variables. Values in the range of 40-70 Mbytes seem to work well on most architectures. As a simple troubleshooting step the user may try adjusting this resource, or the process stack size, for their particular application. Here is a list of suggested runtime resource settings affecting the process and/or thread stack sizes. How to increase the stacksize on different platforms · Compaq limit stacksize unlimited setenv MP\_STACK\_SIZE 17000000 · IBM limit stack size unlimited setenv XLSMPOPTS "stack=40000000" · SGI origin limit stack size unlimited setenv MP\_SLAVE\_STACKSIZE 40000000 · SUN limit stacksize unlimited · PC/Linux limit stacksize unlimited setenv MPSTKZ 40000000 General problems on different platforms Most distributed-memory platforms also provide runtime settings to enable a user to override the multiprocessing defaults and customize the machine parallelism to a particular application. CAM performance can be adversely affected by an incorrect configuration of the machine parallelism. The run scripts provided in the distribution create an executable that will run in a hybrid mode on distributed architectures, using MPI for communication between nodes and OpenMP directives on processes within a node. When running in hybrid mode the user should set the number of MPI tasks per node to be 1. Thread-based OpenMP multitasking will utilize all processors on the node. If the user makes the appropriate changes to the Makefile to disable OpenMP and use only MPI, the number of MPI tasks per node should be set equal to the number of physical processors per node. At this point the model should begin compiling and executing. Appropriate log files will be generated in the /ptmp/$LOGNAME/$CASE directory. After a successful run of the model, the user may edit the namelist variables in run-ibm.csh to better suit their particular needs. After 34
successfully compiling the model, subsequent invocations of the run script will only recompile when the user makes changes to model code. The model should begin execution very quickly after gmake verifies than no code has been changed. In addition to properly configuring machine resources, we've identified the following problems often encountered when building and running CAM on the machines here at NCAR. · PC/Linux The number of underscore characters appended to Fortran external names is different for default configurations of the NetCDF and MPI libraries. libnetcdf.a wants to build with 1 underscore appended to Fortran external names, while libmpich.a wants to build with 2. The default CAM build procedure assumes 1 underscore. You can change this by adding the compiler directive "-Msecond underscore" to the environment variable "USER FLAGS". This directive produces objects with subroutine names have two underscores appended. 2.7 Running CAM as part of the CCSM coupled model system CAM 3.0 is the atmospheric model component of the Community Climate System Model (CCSM), which also includes ocean, land, and sea-ice models, as well as a flux coupler. Details on the use of CCSM may be found in the CCSM User's Guide. Please note that the port of CAM to the CCSM does not use the supported configuration and control mechanisms (configure and build-namelist) described in this guide. However, portions of this User's Guide (e.g. CAM Namelist Variables (B)) may still be of interest to CCSM users. More information on the CCSM can be found on its web page (http://www.ccsm.ucar.edu/models/ccsm3.0/ccsm/). 35
36
Chapter 3 Model Output CAM 3.0 produces a series of NetCDF-format history files containing atmospheric gridpoint data generated during the course of a run. It also produces a series of binary restart files necessary to continue a run once it has terminated successfully and a series of initial conditions files that may be used to initialize new simulations. The formats of these datasets are described below. 3.1 Model History Files History files contain model data values written at specified times during a run. The user can specify the frequency at which the data is written. Options are also available to record averaged, instantaneous, maximum, or minimum values on a field-by-field basis. If the user wishes to see a field written at additional time frequencies (e.g. daily, hourly), additional history files must be declared. History files may be visualized using various commercial or freely available tools. Examples include the "CCSM component model Processing Suite (CMPS)", the NCAR Graphics package, FERRET, ncview, MATLAB, AVS, IDL, and Yorick. For a list of software tools for interacting with NetCDF files, view the UNIDATA NetCDF web-site: http://my.unidata.ucar.edu/content/software/netcdf/software.html. Aside from the default history file series the user may specify up to five additional history file series for a total of up to six history file series. The frequency at which these history file series are written as well as the contents and averaging options are specified using the same namelist variables described above for modifying the first history file series. Table 3.1 lists the fields that can be output on any of the six history files as well as which fields are output by default on the first file series. 3.1.1 Master Field List Table 3.1 contains a list of fields, referred to as the "Master Field List", that can be written to history files. The first column lists the names of the output variables. The second column shows the mathematical symbol associated with the history field, as given in Collins et al. [2004]. The third column provides a brief description of the field. 37
In the fourth column shows the number of levels for the field. A "1" indicates a single-level field and an "N" indicates a multilevel field (on plev vertical levels). The fifth column shows the default averaging flag. The flags available are: Instantaneous (I), Average (A), Maximum (X), and Minimum (M). The sixth column in the table shows the physical units associated with each field. The last column indicates whether the field will automatically be included on the first history file series. Fields not on by default may be included via the namelist variable FINCL1. Conversely, any default fields may be removed using namelist variable FEXCL1. The fields are presented in alphabetical order.
Table 3.1: Master Field List
Field Name AERASM v AERFWD v AEROD v AERSSA v ALDIF ALDIR ASDIF ASDIR BGOD v CAROD v CGH CGQ CGS CLDFRQ CLDHGH CLDICE CLDLIQ CLDLOW CLDMED CLDST
Symbol
Field Description Total Aerosol Asymmetry Parameter in visible Total Aerosol Forward Scattering in visible Total Aerosol Optical Depth in visible Total Aerosol Single Scattering Albedo in visible albedo: longwave, diffuse albedo: longwave, direct albedo: shortwave, diffuse albedo: shortwave, direct Background Aerosol Optical Depth in visible Carbon Optical Depth in visible Counter-gradient term for heat in PBL Counter-gradient term for moisture in PBL Counter-gradient coeff on surface kinematic fluxes Frequency of occurance of clouds (CLOUD ї 0.01) Vertically-integrated high cloud Grid box averaged ice condensate amount Grid box averaged liquid condensate amount Vertically-integrated low cloud Vertically-integrated mid-level cloud Stratus cloud fraction
NL AF Units 1 I None 1 I None 1 I None 1 I None 1 A1 1 A1 1 A1 1 A1 1 I None 1 I None 27 A K/m 27 A 1/m 27 A s/m2 26 A fraction 1 A fraction 26 Ak g/kg 26 A kg/kg 1 A fraction 1 A fraction 26 A fraction
Default yes yes yes yes yes
38
Field Name CLDTOT CLOUD CME CMFDQ CMFDQR CMFDT CMFLQ CMFMC CMFSL CNVCLD CONCLD DCCLDICE DCCLDLIQ DCQ DISED DLSED DQP DQSED DTCOND DTH DTV DTVKE DUH DUSTOD v DUV DVH DVV EFFCLD EMIS ENGYCORR
Symbol
Field Description Vertically-integrated total cloud Cloud fraction Rate of cond-evap within the cloud Q tendency - Hack convection Q tendency - shallow convection rainout T tendency - Hack convection Moist convection total water flux Moist convection mass flux Moist convection liquid water static energy flux Vertically integrated convective cloud amount Convective cloud cover CLDICE tendency due to moist processes CLDLIQ tendency due to moist processes Q tendency due to moist processes Cloud ice tendency from sedimentation Cloud liquid tendency from sedimentation Specific humidity tendency due to precipitation Water vapor tendency from cloud sedimentation T tendency - moist processes T horizontal diffusive heating T vertical diffusion dT/dt vertical diffusion KE dissipation U horizontal diffusive heating Dust Optical Depth in visible U vertical diffusion V horizontal diffusive heating V vertical diffusion Effective cloud fraction cloud emissivity Energy correction for over-all conservation
NL AF Units 1 A fraction 26 A fraction 26 A kg/kg/s
26 A kg/kg/s 26 A kg/kg/s
26 A 27 A 27 A 27 A
K/s W/m2 kg/m2/s W/m2
1 A fraction
26 A fraction 26 A kg/kg/s
26 A kg/kg/s
26 A kg/kg/s 26 A kg/kg/s
26 A kg/kg/s
26 A kg/kg/s
26 A kg/kg/s
26 A K/s 26 A K/s 26 A K/s 26 A K/s
26 A 1I 26 A 26 A 26 A 26 A 26 A 26 A
K/s None m/s2 K/s m/s2 fraction 1 W/m2
Default yes yes yes yes yes yes yes yes yes yes yes
39
Field Name ETADOT EVAPPCT EVAPPREC EVAPSNOW FICE FLN200 FLN200C FLNS FLNSC FLNSICE FLNSLND FLNSOCN FLNSOI FLNT FLNTC FLUT FLUTC FRACW frc day FSACI FSACW FSAUT FSDS FSDSC FSN200 FSN200C FSNIRTOA
Symbol
Field Description Vertical (eta) velocity Percentage of Zhang-McFarlane precipitation going into evaporation Rate of evaporation of falling precip Rate of evaporation of falling snow Fractional ice content within cloud Net longwave flux at 200 mb Clearsky net longwave flux at 200 mb Net longwave flux at surface Clearsky net longwave flux at surface FLNS over sea ice FLNS over land FLNS over open ocn FLNS over open ocn and ice Net longwave flux at top of model Clearsky net longwave flux at top of model Upwelling longwave flux at top of model Clearsky upwelling longwave flux at top of model Relative importance of rain accreting liquid Portion of time column is lit Relative importance of snow accreting ice Relative importance of snow accreting liquid Relative importance of ice autoconversion Downwelling solar flux at surface Clearsky downwelling solar flux at surface Net shortwave flux at 200 mb Clearsky net shortwave flux at 200 mb Net near-infrared flux (Nimbus-7 WFOV) at top of atmosphere
NL AF Units 27 A 1/s 1 A percent 26 A kg/kg/s 26 A kg/kg/s 26 A fraction 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2 26 A fraction 1 I None 26 A fraction 26 A fraction 26 A fraction 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2
Default yes yes yes yes yes yes yes yes yes yes
40
Field Name FSNRTOAC FSNRTOAS FSNS FSNSC FSNSICE FSNSLND FSNSOCN FSNSOI FSNT FSNTC FSNTOA FSNTOAC FU FV FWAUT GCLDLWP HEVAP HKEIHEAT HKFLXPRC HKFLXSNW HKNTPRPD HKNTSNPD HMELT HPROGCLD HR HREPART HSED ICEFRAC
Symbol
Field Description Clearsky net near-infrared flux (Nimbus-7 WFOV) at top of atmosphere Net near-infrared flux (ї= 0.7 microns) at top of atmosphere Net solar flux at surface Clearsky net solar flux at surface FSNS over sea ice FSNS over land FSNS over open ocn FSNS over open ocn and ice Net solar flux at top of model Clearsky net solar flux at top of model Net solar flux at top of atmosphere Clearsky net solar flux at top of atmosphere Zonal wind forcing term Meridional wind forcing term Relative importance of liquid autoconversion Grid-box cloud water path Heating from evaporation of falling precip Heating by ice and evaporation in HK convection Flux of precipitation from HK convection Flux of snow from HK convection Net precipitation production from HK convection Net snow production from HK convection Heating from snow melt Heating from prognostic clouds Heating rate needed for d(theta)/dt computation Heating from cloud ice/liquid repartitioning Heating from cloud sediment evaporation Fraction of sfc area covered by seaice
NL AF Units Default 1 A W/m2
1 A W/m2
1 A W/m2 yes 1 A W/m2 yes 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2 yes 1 A W/m2 yes 1 A W/m2 yes
1 A W/m2 yes 1 A W/m2 yes
26 I 26 I 26 A
m/s m/s fraction
26 A gram/m2 yes 26 A W/kg
26 A W/kg
27 A kg/m2/s
27 A kg/m2/s 26 A kg/kg/s
26 A kg/kg/s
26 A 26 A 26 A
W/kg W/kg K/s
26 A W/kg
26 A W/kg
1 A fraction yes
41
Field Name ICIMR ICLDIWP ICLDLWP ICWMR KVH KVM LANDFRAC LANDMCOS LHFLX LHFLXICE LHFLXLND LHFLXOCN LHFLXOI LPSTEN LWC LWCF LWSH MBCPHI V MBCPHO V MBG V MDUST1 V MDUST2 V MDUST3 V MDUST4 V MOCPHI V MOCPHO V MQ
Symbol
Field Description Prognostic in-cloud ice mixing ratio In-cloud ice water path In-cloud cloud water path (liquid and ice) Prognostic in-cloud water mixing ratio Vertical diffusion diffusivities (heat/moisture) Vertical diffusion diffusivities (momentum) Fraction of sfc area covered by land Land ocean transition mask: ocean (0), continent (1), transition (0-1) Surface latent heat flux LHFLX over sea ice LHFLX over land LHFLX over open ocn LHFLX over open ocn and ice Surface pressure tendency Liquid Water Content Longwave cloud forcing Liquid water scale height Mass of BCPHI in and below layer Mass of BCPHO in and below layer Mass of Background Aerosol in and below layer Mass of Dust bin 1 in and below layer Mass of Dust bin 2 in and below layer Mass of Dust bin 3 in and below layer Mass of Dust bin 4 in and below layer Mass of OCPHI in and below layer Mass of OCPHO in and below layer Water vapor mass in layer
NL AF Units Default 26 A kg/kg 26 A gram/m2 yes 26 A gram/m2 yes 26 A kg/kg 27 A m2/s 27 A m2/s 1 A fraction yes 1 I unitless 1 A W/m2 yes 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2 yes 1 A Pa/s 26 A kg/m3 1 A W/m2 yes 1 Am 26 I Kg/m^2 26 I Kg/m^2 26 I Kg/m^2 26 I Kg/m^2 26 I Kg/m^2 26 I Kg/m^2 26 I Kg/m^2 26 I Kg/m^2 26 I Kg/m^2 26 A kg/m2
42
Field Name MSO4 MSSLT V MSUL V MVOLC NSTEP O3VMR OCNFRAC OMEGA OMEGA500 OMEGA850 OMEGAT OMEGAU PBLH PBOT PCSNOW PDELDRY PHIS PRECC PRECCFRQ PRECCINT PRECCav PRECL PRECLFRQ PRECLINT PRECLav
Symbol
Field Description Mass concentration of SO4 Mass of Sea Salt in and below layer Mass of Sulfate in and below layer Mass of Volcanic Aerosol in layer Model timestep Ozone volume mixing ratio Fraction of sfc area covered by ocean Vertical velocity (pressure) Vertical velocity at 500 mbar pressure surface Vertical velocity at 850 mbar pressure surface Vertical heat flux Vertical flux of zonal momentum PBL height Lowest model level pressure Snow fall from prognostic clouds Dry pressure difference between levels Surface geopotential Convective precipitation rate Convective precipitation frequency (fraction of time where rate is ї 0.10mm/hr) Convective precipitation rate (less than 0.10mm/hr is set to zero ­ to get intensity divide by PRECCFRQ) Average large-scale precipitation Large-scale (stable) precipitation rate Large-scale (stable) precipitation frequency (fraction of time where rate is ї 0.05mm/hr) Large-scale (stable) precipitation rate (less than 0.05mm/hr is set to zero ­ to get intensity divide by PRECLFRQ) Average convective precipitation
NL AF Units Default 26 A gram/cm3 26 I Kg/m^2
26 I 26 I 1A 26 A 1A
Kg/m^2 Kg/m^2 timestep m3/m3 fraction yes
26 A Pa/s yes 1 A Pa/s
1 A Pa/s
26 A K Pa/s yes
26 A K Pa/s
1 Am
yes
1 A Pa
1 A m/s
26 A Pa
yes
1 I m2/s2 yes
1 A m/s
yes
1 Af raction
1 A mm/hr
1 A m/s
1 A m/s
yes
1 A fraction
1 A mm/hr
1 A m/s
43
Field Name PRECSC PRECSED PRECSH PRECSL PRECT PRECTMX PRODPREC PS PSDRY PSL PS match Q Q200 Q850 QBOT QC QFLX QPERT QRL QRS RAINSED REI REL RELHUM SETLWP SFCLDICE SFCLDLIQ SFQ
Symbol
Field Description Convective snow rate (water equivalent) Precipitation from cloud sedimentation Shallow Convection precipitation rate Large-scale (stable) snow rate (water equivalent) Total (convective and large-scale) precipitation rate Maximum (convective and largescale) precipitation rate Rate of conversion of condensate to precip Surface pressure Surface pressure Sea level pressure Surface Pressure from aerosol climatology Specific humidity Specific Humidity at 700 mbar pressure surface Specific Humidity at 850 mbar pressure surface Lowest model level water vapor mixing ratio Q tendency - shallow convection LW export Surface water flux Perturbation specific humidity (eddies in PBL) Longwave heating rate Solar heating rate Rain from cloud liquid sedimentation effective ice particle radius effective liquid drop radius Relative humidity Prescribed liquid water path CLDICE surface flux CLDLIQ surface flux Q surface flux
NL AF Units Default
1 A m/s
yes
1 A m/s
1 A m/s
yes
1 A m/s
yes
1 A m/s
1 Xm /s
26 A kg/kg/s
1 A Pa
yes
1 A Pa
yes
1 A Pa
yes
1 I N/m^2
26 A kg/kg yes 1 A kg/kg
1 A kg/kg
1 A kg/kg
26 A kg/kg/s yes
1 A kg/m2/s yes 1 A kg/kg
26 A K/s
yes
26 A K/s
yes
1 A m/s
26 A micron 26 A micron 26 A percent yes 26 A gram/m2 1 A kg/m2/s yes 1 A kg/m2/s yes 1 A kg/m2/s yes
44
Field Name SGH SHFLX SHFLXICE SHFLXLND SHFLXOCN SHFLXOI SICTHK SNOWHICE SNOWHLND SNOWSED SOLIN SOLL SOLLD SOLS SOLSD SRFRAD SSLTOD v SST SULFANT SULFBIO SULFMMR SULOD v SWCF T T300 T850 TAUGWX TAUGWY TAUTMSX TAUTMSY
Symbol
Field Description Standard deviation of orography Surface sensible heat flux SHFLX over sea ice SHFLX over land SHFLX over open ocn SHFLX over open ocn and ice Sea ice thickness Water equivalent snow depth Water equivalent snow depth Snow from cloud ice sedimentation Solar insolation Solar downward near infrared direct to surface Solar downward near infrared diffuse to surface Solar downward visible direct to surface Solar downward visible diffuse to surface Net radiative flux at surface Sea Salt Optical Depth in visible sea surface temperature Anthropogenic sulfate mass mixing ratio Biogenic sulfate mass mixing ratio Sulfate mass mixing ratio Sulfate Optical Depth in visible Shortwave cloud forcing Temperature Temperature at 300 mbar pressure surface Temperature at 850 mbar pressure surface Zonal gravity wave surface stress Meridional gravity wave surface stress Zonal turbulent mountain surface stress Meridional turbulent mountain surface stress
NL AF Units 1I m 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2 1 A W/m2 1 Am 1 Am 1 Am 1 A m/s
1 A W/m2 1 A W/m2
1 A W/m2
1 A W/m2
1 A W/m2
1A 1I 1A 26 A
W/m2 None K kg/kg
26 A 26 A 1I 1A 26 A 1A
kg/kg kg/kg None W/m2 K K
1 AK
1 A N/m2 1 A N/m2
1 A N/m2
1 A N/m2
Default yes yes yes yes yes yes yes yes
45
Field Name Symbol TAUVIS TAUX TAUY TBOT TEFIX TEINP TEOUT TGCLDCWP TGCLDIWP TGCLDLWP TMQ TPERT TREFHT TREFHTMN TREFHTMX TREFMNAV TREFMXAV TS TS1 TS2 TS3 TS4 TSICE TSMN TSMX TT TTEND TTGWORO U
Field Description Total column aerosol extinction, vis band [aerosol optical depth] Zonal surface stress Meridional surface stress Lowest model level temperature Total energy after fixer Total energy of physics input Total energy of physics output Total grid-box cloud water path (liquid and ice) Total grid-box cloud ice water path Total grid-box cloud liquid water path Total (vertically integrated) precipitatable water Perturbation temperature (eddies in PBL) Reference height temperature Minimum reference height temperature over output period Maximum reference height temperature over output period Average of TREFHT daily minimum Average of TREFHT daily maximum Surface temperature (radiative) TS1 subsoil temperature TS2 subsoil temperature TS3 subsoil temperature TS4 subsoil temperature Ice temperature Minimum surface temperature over output period Maximum surface temperature over output period Eddy temperature variance T tendency T tendency - orographic gravity wave drag Zonal wind
NL AF Units Default 1 A unitless
1 A N/m2 yes 1 A N/m2 yes 1 AK 1 A W/m2 1 A W/m2 1 A W/m2 1 A gram/m2
1 A gram/m2 yes
1 A gram/m2 yes
1 A kg/m2 yes
1 AK
1 AK
yes
1 MK
1 XK
1 AK
1 AK
1 AK
yes
1 AK
1 AK
1 AK
1 AK
1 AK
1 MK
yes
1 XK
yes
26 A K2 26 A K/s 26 A K/s
26 A m/s
yes
46
Field Name U200 U850 UBOT US USTAR UTEND UTGWORO UU V V200 V850 VBOT VD01 VDCLDICE VDCLDLIQ VOLCOD v VQ VS VT VTEND VTGWORO VU VV VZ WLWC WREL WSPEED Z050 Z3
Symbol
Field Description Zonal wind at 200 mbar pressure surface Zonal wind at 850 mbar pressure surface Lowest model level zonal wind Zonal wind, staggered Surface friction velocity U tendency U tendency - orographic gravity wave drag Zonal velocity squared Meridional wind Meridional wind at 200 mbar pressure surface Meridional wind at 850 mbar pressure surface Lowest model level meridional wind Vertical diffusion of Q Vertical diffusion of CLDICE Vertical diffusion of CLDLIQ Volcanic Aerosol Optical Depth in visible Meridional water transport Meridional wind, staggered Meridional heat transport V tendency V tendency - orographic gravity wave drag Meridional flux of zonal momentum Meridional velocity squared Meridional transport of geopotential energy Weighted Liquid Water Content, prognostic (by CLDFRQ) Weighted effective radius (by CLDFRQ) Horizontal total wind speed Geopotential Z at 50 mbar pressure surface Geopotential Height (above sea level)
NL AF Units Default 1 A m/s
1 A m/s
1A 26 A 1A 26 A 26 A
m/s m/s m/s m/s2 m/s2
26 A m2/s2 yes
26 A m/s
yes
1 A m/s
1 A m/s
1 A m/s
26 A 26 A 26 A 1I
kg/kg/s yes kg/kg/s kg/kg/s None
26 A 26 A 26 A 26 A 26 A
m/skg/kg yes m/s K m/s yes m/s2 m/s2
26 A m2/s2 yes
26 A m2/s2 yes 26 A m2/s
26 A kg/m3
26 A um
26 X m/s 1 Am
26 A m
yes
47
Field Name Z300 Z500 Z700 ZBOT ZMDLF ZMDQ ZMDT ZMEIHEAT ZMFLXPRC ZMFLXSNW ZMNTPRPD ZMNTSNPD ZZ
Symbol
Field Description Geopotential Z at 300 mbar pressure surface Geopotential Z at 500 mbar pressure surface Geopotential Z at 700 mbar pressure surface Lowest model level height Detrained liquid water from ZM convection Q tendency - Zhang-McFarlane moist convection T tendency - Zhang-McFarlane moist convection Heating by ice and evaporation in ZM convection Flux of precipitation from ZM convection Flux of snow from ZM convection Net precipitation production from ZM convection Net snow production from ZM convection Eddy height variance
NL AF Units 1 Am 1 Am 1 Am 1 Am 26 A kg/kg/s 26 A kg/kg/s 26 A K/s 26 A W/kg 27 A kg/m2/s 27 A kg/m2/s 26 A kg/kg/s 26 A kg/kg/s 26 A m2
Default
3.1.2 History Files 2 through 6 Up to six different types of history files may be written out by the model during a model run. The capability to write additional history files provides the user with the flexibility to vary the frequency at which various history data are written. Additional files may contain the same or different fields as compared with the first history file. These fields may be written on different timesteps, and have different averaging periods. Furthermore, each file may contain a different number of time samples.
3.1.3 Changing the characteristics of history files There are several ways that namelist options can modify the characteristics of the output fields on history tapes. Output fields can be added or deleted from a file, the averaging flag can be changed and the output frequency can be varied. In addition, the number of time-samples on a file and the precision of the output data (double or single NetCDF) can be changed. To add additional fields to the first history file, the user should use the namelist variable FINCL1. FEXCL1 can be used to delete fields that are on the default list of fields on the first history file series. The averaging flag may also be specified with the FINCL1 option and determines how the data is averaged over the output frequency. Values recorded for fields on a history file can be represented in one of four different ways. Data may be time averaged since the last write to
48
the history file, instantaneous, or appear as a point-by-point maximum or minimum over the time interval. The representation may be specified in the namelist by including a colon followed by the single character flag for each averaging type after the field name. The characters are as follows: 'A' means averaged over the interval, 'I' for instantaneous, 'M' for point-by-point minimum, and 'X' for point-by-point maximum. An example of this specification would be: FINCL1 = 'T:I' This specifies that temperature is to be recorded as instantaneous values on the first history file. Other namelist variables that modify history file behavior are NHTFRQ(6) (frequency of history file writes), MFILT(6) (number of time samples per history file), and NDENS(6) (packing density). Please see Table B.1 for more information. 3.1.4 Naming the History Files History volumes will be named according to the history filename specifier. The history filename name specifier may be specified using the namelist variable HFILENAME SPEC (6), but by default the first history file series will contain monthly output and the filenames will be of the form caseid.cam2.h0.yyyy-mm.nc where caseid, yyyy, and mm correspond to the case-name, current year, and current month respectively. For example, if caseid="cambld", and current date is September, 1989 the filename becomes cambld.cam2.h0.1989-09.nc Non-monthly file-series are named with a full date expression as follows: caseid.cam2.h#.yyyy-mm-dd-sssss.nc Here, # is the file series number minus one, dd is the current day, and sssss is the number of seconds into the current day. For example, for the second file-series and a current date of September, 1, 1989, 0Z the filename becomes: cambld.cam2.h1.1989-09-01-00000.nc 3.2 Model generated initial condition dataset files During a model simulation, initial condition datasets are generated periodically by default. These datasets are simply history files containing instantaneous values for only those fields that are required to begin an initial run. The naming convention for these files (which is different for the other history files) is $CASE.cam2.i.yyyy-mm-dd-sssss.nc, where $CASE is the caseid, yyyy is the year (note, more than 4 digits will be used if needed), mm is the month, dd is the day and sssss is the seconds. The output frequency of the files is controlled by namelist variable INITHIST and is independent of the output frequency of other history files. 3.3 Restart Datasets There are three types of restart datasets generated by the model: master, secondary, and history buffer restart files. Each dataset is in binary format and contain grid-point data and other information necessary to continue or branch a model run. 49
Upon restart, a simple ASCII text file (the "restart pointer file") is read to obtain the full pathname of the most recently written master restart file. Only the name of the master restart file is needed as input for a continuation run. The other files needed for restart (such as secondary restart files, or history files that need to be opened) are also listed in the restart pointer file. The Master restart file itself includes the full archive path to the files that actually need to be opened. Master restart files are always written during a model run. A secondary restart file is written if absorptivity/emissivity is not be calculated on the first timestep after restart, and therefore must be saved on a restart dataset. For a stand-alone run this occurs if the first history file series write frequency, NHTFRQ(1), is not a multiple of the absorptivity/emissivity calculation frequency, IRADAE (note that for a CCSM flux coupled run, only the flux coupler determines when the restart files are written). It is advisable to avoid this situation if possible, since this dataset is relatively large even for the standard T42 model. A history buffer restart file is written in order to retain the accumulated values in the history buffers if restart files are to be written on a timestep when one or more history file time samples are not written. A separate restart dataset is written for each history file. Each history buffer restart file contains the portion of the history buffers pertaining to that history file. All restart files have names of the form $CASE.cam2.r.yyyy-mm-dd-sssss, but with the ".r." changed to the appropriate restart filename. For example, ".r." is for the master restart filename, while , ".ra." corresponds to the absorptivity/emissivity restart filename, and ".rh0." is the first history file series restart filename. In the root name, $CASE refers to the caseid, yyyy corresponds to the year (note more than 4 digits for the year will be used if necessary), mm is the month, dd is the day and sssss is the seconds of the date yyyymmdd. The following is an example of the restart files written during a simulation. · $CASE.cam2.r.1001-01-3600 - master restart file · $CASE.cam2.ra.1001-01-3600 - absorptivity/emissivity restart file · $CASE.cam2.rh0.1001-01-3600 - history buffer restart file for first history file · $CASE.cam2.rh1.1001-01-3600 - history buffer restart file for second history file 3.4 Mass Store Archiving Users running CAM on NCAR machines have the option of archiving model history files to the NCAR Mass storage system (MSS). If history files, restart datasets, and initial conditions datasets are to be archived, they will be transferred (as a background process) to the MSS as they are completed. If namelist variable MSS IRT is zero, history and restart files will not be archived. Mass Store pathnames for these transfers are generated using the ARCHIVE DIR namelist setting. By default, ARCHIVE DIR is set to /$USERNAME/csm/$CASE/atm/hist. As a result history files will be archived in the Mass Store directory /$USERNAME/csm/$CASE/atm/hist Restart files will be archived in the Mass Store directory /$USERNAME/csm/$CASE/atm/rest. And finally initial files will be archived in the Mass Store directory 50
/$USERNAME/csm/$CASE/atm/init. $USERNAME is the upper-case equivalent of the user's login name, i.e., the user's root directory on the Mass Store System, and $CASE is the case identifier and is set via the namelist input. It is recommended that the user specify a non-blank write password using the namelist variable MSS WPASS. File passwords are the only form of security available on the Mass Storage System. If the write password is not set, any other user can overwrite or change the files after they have been archived. 3.5 Model Vertical Coordinate The vertical coordinate is a hybrid sigma-pressure system. In this system, the upper regions of the atmosphere are discretized by pressure only. Lower vertical levels use the sigma (i.e. p/ps) vertical coordinate smoothly merged in, with the lowest levels being pure sigma. A schematic representation of the hybrid vertical coordinate and vertical indexing is presented below. Both input and output datafiles follow this format as well as internal model datastructures. Pressure is defined as: p(i,j,k)= AkP0+ BkPs(i,j) where p is the pressure at a given level and latitude, longitude grid point. The coefficients A, B and P0are constants. Ps is the model's current surface pressure. P0 is set in the model code. The input model initial conditions dataset sets A and B through the variables hyam, hyai, hybm, and hybi. The subscript "i" refers to interface levels, and "m" refers to the mid-point levels. "hyam" then refers to Hybrid level "A" coefficient on the interfaces. More details on the theoretical nature of the vertical coordinate system can be found in Collins et al. [2004]. 51
Pressure
Level Interface Index Index
2.917 mb
1/2
1
Pure Pressure Region
1 1/2 2 2 1/2
83.1425 mb Hybrid Sigma-Pressure Region Pure Sigma Region surface s
k-3/2 k-1 k-1/2 k k+1/2 k+1 k+3/2
Fs FL Fs FL
K-3/2 K-1 K-1/2 K K+1/2
Mc Ac Mc
U,V,T, q, , , ,
Figure 3.1: Hybrid vertical coordinate
52
Chapter 4 Simple Code Modifications
The most common changes to the model are the addition of new output variables, the addition of transported constituents, the modification of history file contents, the modification of the model resolution, and the addition of a new parameterization. This section provides some guidelines for making these kinds of changes. For more details on the scientific and algorithmic structure of the model see the CAM 3.0 Scientific Description.
4.1 Using the Scripts with Modified Code If the user wishes to include modified code, a disk directory or directories should first be created where all the modified code will reside. See the "-usr src" option in the section titled The configure utility (2.1) for documentation on configuring the model to use directories with modified source code.
4.2 Adding New Output Variables
This section describes how to add a variable to a history file. If the field is in the Master Field List (see Table 3.1), the user must ensure that there is an uncommented outfld call for that field and must also add it to the history output via namelist variable(s) FINCL(1-6). If the field is not on the Master Field List, the user must add it to the list by inserting an addlfd call. Six pieces of information are passed to addfld in an argument list:
1. Field name: 8-character field name, left-justified, alphanumeric or spaces only. 2. Field units: 8-character units description. See Table 3.1 3. Number of vertical levels in the field. 4. Default averaging flag. See Section 3.1.1 for more information. 5. Field descriptor: up to 128-characters 6. Parallel decomposition type (i.e. is this a physics or dynamics variable)
Please see the file history.F90 for more information on the addfld interface. Two examples extracted from the model are shown below.
call addfld('TS call addfld('U
', 'K ', 'K
', 1,'A', 'Surface temperature', phys\_decomp )
', plev,'A', 'Zonal wind'
, dyn\_decomp )
53
Table 4.1: Units of History File Fields
Abbreviation Description
m
meter
kg
kilogram
s
second
K
degree Kelvin
percent
percent
fraction
fraction
gram
gram
um
micro meter
N
Newton
Pa
Pascal
W
Watt
The user must then add an outfld call for the field at an appropriate location in the code. For example, the outfld call for the field T, taken from diagnostics.F90, is shown below:
call outfld('T
', state\%t, pcols, lchnk )
The arguments in the call to outfld are the 8-character field name, the variable array in which it is stored, the first dimension of the data array, and the chunk index. Once these steps are taken, the field may be added to the desired history file by using namelist variable FINCL(1-6).
4.3 Trouble-Shooting Model Changes If the cause of abnormal termination is unclear, the user should first ensure that the model is run single-threaded with SPMD off. Abnormal termination in a multi-tasked job can result in confusing ancillary error messages. We address several possible causes of model failure. Resource allocation errors will be addressed first, followed by remedies for suspected coding errors. Finally, analysis tools are described for physics formulation errors (i.e., where there is an error in modifications to a prognostic variable calculation). 4.3.1 Resource Allocation Errors A system resource problem which may occur on linux architectures is that the default stack size on linux machines is sometimes too small for larger resolution runs or when running on multiple processors. The model usually fails with a segmentation fault. The user should try increasing the stack size if this problem occurs. The stack size can be set to its maximum by using the limit command. Typing limit alone will print the system resource limits. To set the stack size to its maximum type limit stacksize unlimited . 54
When running the message passing code on multiple processors it is necessary to place the limit command in the user's shell startup script. Since the message passing software usually starts new processes, the user must make sure that these processes have the larger stack size when started by MPI. An easy way to determine that new shells have the larger stack size is to execute the command rsh machine limit (where machine is the name of a computer on which to start the remote shell.) Once the stack size has been increased try running the model again. If the stack size was too small before it should run to completion. 4.3.2 Coding Errors We suggest that for debugging purposes only statically allocated memory locations and/or stack space be initialized to "indefinite". Furthermore,array bounds checking should be turned on if possible. The standard Makefile achieves this if configure is invoked with the -debug option. If the model is running but producing incorrect or suspicious history files, a quick and easy-touse diagnostic program, cprnc, is available. cprnc is available in the directory models/atm/cam/tools. This program provides a Statistical Analysis of differences in history file data. No command line arguments are required. cprnc compares fields of the same name on each file, printing out statistics about the number of differences found, location and magnitude of worst absolute difference, location and magnitude of worst relative difference, RMS difference, maximum and minimum field values, and average field values. 4.4 Porting the model to new resolutions If the user needs to run the model at resolutions that aren't provided in the above set of datasets they will need additional datasets. The user will need to create an atmospheric initial-condition dataset as well as a SST dataset for this resolution. The user could do this by interpolating the datasets that are provided. Currently we do not provide tools to do this interpolation. Also when running at a different resolution land model datasets will need to be created from the high resolution datasets. These are available in the download section of the main CAM web page (http://www.ccsm.ucar.edu/models/atm-cam). 55
56
Appendix A Glossary
Name branch run CAM case cc CCM CCSM CPP continuation run CSEG CLM CPU CSIM
Synopsis A type of continuation run of the CAM. A branch run starts a new case using the restart files from a previous model run. This is used primarily when you wish to exactly reproduce a control simulation, but change the output fields. Community Atmosphere Model; the latest atmosphere model code which can be run as part of the CCSM or as a stand-alone atmosphere model for climate prediction. A term used to denote a model experiment, including one initial run and as many continuation runs as required to conclude the experiment. A model case is cataloged using the CASEID namelist variable. By default the caseid is included in the output filenames and mass store archive path. "C" language compiler. Community Climate Model; the predecessor model code of CAM used in making climate predictions. Community Climate System Model. The set of geophysical models for atmosphere, land, ocean, and sea-ice to model the climate system. CAM is the atmosphere model component for the CCSM. C preprocessor. A type of run that uses a restart file from a previous run to initialize the data fields (no initial dataset is read). Restart and branch runs are each possible types of a continuation run. CCSM software engineering Group. The group of Software Developers at NCAR responsible for maintaining and developing the CCSM codes. The Community Land Model a land surface model. Central Processing Unit. Community Sea-Ice Model. 57
Name distributed memory DOM ECMWF ESMF FV flux-coupled GNU gzip header file heap history file initial run LSM module MPI MPMD
Synopsis Multi-processing on multiple CPU's using the SPMD Programming Model. Data Ocean Model. Ocean component of stand-alone CAM that reads in SST information from an input dataset. European Center for Medium Range weather forecasting Earth System Modeling Framework The Finite-Volume (also referred to as Lin-Rood) dynamical core. A simulation with the atmosphere model where the model is linked to a system of geo-physical models (land, ocean, and seaice). When run in this manner each seperate component is built as a seperate executable, and each component communicates with each other in Multiple Program - Multiple Data (MPMD) mode. See also CCSM. GNU's not UNIX. A set of Open-Source freely provided utilities for UNIX. GNU decompression utility similar to UNIX uncompress. Takes a file and inflates it to it's full size so that it can be used. Files are compressed to save disk space and save on network file transfer times. A file containing CPP tokens to set the particular model resolution and configuration named with a ".h" suffix (e.g. misc.h). Memory that is dynamically allocated by the system. Unlike stack memory, heap memory can be allocated or de-allocated at any point during program execution. The output NetCDF dataset that the model produces to record the model simulation field values with time. A startup simulation using a initial-condition dataset. The NCAR Land Surface Model. This model was used with the CCM the predecessor to CAM. A FORTRAN-90 construct containing data and subroutines and functions that operate on that data. This is a somewhat objectoriented approach to datastructures. The data can be specified as private to the module or public for access by other subroutines. Outside subroutines can specify the limited set of variables they wish to capture. This ability provides a better approach to handling data and is the preferred method for dealing with data over COMMON blocks. Message Passing Interface. A standardized library for distributed memory Parallel Processing. Multiple Program Multiple Data. Parallel programming model with several distinct executable programs operating on different sets of data.
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Name mpxlf90 mpxlf90 r MSS multi-tasked NCAR NetCDF OpenMP PBL pcnst pgf90 plat plev plon restart run single-threaded shared-memory SLT SPMD stack stand-alone STDERR STDOUT transform grid UNIDATA UNIX
Synopsis FORTRAN-90 compiler for IBM AIX with message passing (MPI) libraries included. Thread-safe FORTRAN-90 compiler for IBM AIX with message passing (MPI) libraries included, and allowing for OpenMP threading. The NCAR Mass Store System. A program configured to execute on several distributed processors simultaneously. See distributed memory. National Center for Atmospheric Research Network Common Data Format. Self describing, platform independent binary data format (created by UNIDATA). Open specification for Multi-Processing. Set of compiler directives for shared-memory parallel processing, that is supported by most compiler venders. Planetary Boundary Layer. Number of advected constituents carried in the model. Portland Group's FORTRAN-90 compiler, Number of Gaussian latitudes on the transform grid. Number of vertical model levels. Number of longitudes on the transform grid A type of continuation run of the CAM. A restart run continues a previous run from its point of termination, by reading most recent restart Parallel-processing term. Refers to the parts of shared memory processed code that executes on only one processor. Parallel-processing term. Refers to using a machine where multiple CPU's share the same memory. Semi-Lagrangian Transport. Single Program Multiple Data. Memory local to a subroutine or function. Running the model not in flux-coupled mode as described above, but as a single-executable with land, thermodynamic sea-ice, and data ocean models as subroutines of the main executable. standard error. Output stream that error messages are sent to. Usually, this is the users terminal. Standard output. Default output stream that messages are sent to. Usually, this is the users terminal. A grid used to evaluate all nonlinear and diabatic forcing terms in physical space. University Atmospheric Data access project funded by the National Science Foundation (NSF). A modern operating system shared and supported by most supercomputers. 59
60
Appendix B CAM Namelist Variables A CAM model run is controlled using the CAM build-namelist facility described in Section 2.2. The focus of this appendix is to provide a reference for the variables that may be set through the use of build-namelist's -namelist option. Please see Table B.1 in the section named Complete list of CAM namelist variables (B.13) for a list of all valid namelist variables in alphabetical order. We also present a set of convenient subject-oriented lists broken into the following categories: · CAMEXP run type namelist variables (B.1) · CAMEXP time management namelist variables (B.2) · CAMEXP input dataset namelist variables (B.3) · CAMEXP history file namelist variables (B.4) · CAMEXP mass store control namelist variables (B.5) · CAMEXP restart file namelist variables (B.6) · CAMEXP dynamics namelist variables (B.7) · CAMEXP physics namelist variables (B.8) · CAMEXP non-water constituent namelist variables (B.9) · CAMEXP memory namelist variables (B.10) · CAMEXP performance tuning namelist variables (B.11) · CAMEXP orbital parameter namelist variables (B.12) When using the pdf or html versions of this document, you may click on any variable name to get a complete description. B.1 CAMEXP run type namelist variables CASEID, CTITLE, NSREST, PERPETUAL RUN, PERPETUAL YMD B.2 CAMEXP time management namelist variables CALENDAR, DTIME, NELAPSE, NESTEP, REF TOD, REF YMD, START TOD, START YMD, STOP TOD, STOP YMD, 61
B.3 CAMEXP input dataset namelist variables ABSEMS DATA, AEROPTICS, BNDTVAER, BNDTVCARBONSCALE, BNDTVDMS, BNDTVGHG, BNDTVG, BNDTVOXID, BNDTVO, BNDTVSCON, BNDTVSF6, BNDTVSOX, BNDTVS, BNDTVVOLC, CO EMIS, ISCCPDATA, NCDATA, OZNCYC, SOIL EROD, SSTCYC
B.4 CAMEXP history file namelist variables
AVGFLAG PERTAPE (6), EMPTY HTAPES, FEXCL1, FEXCL2, FEXCL3, FEXCL4, FEXCL5, FEXCL6,
FINCL1, FINCL2, FINCL3, FINCL4, FINCL5, FINCL6,
FINCL1LONLAT, FINCL2LONLAT,
FINCL3LONLAT, FINCL4LONLAT, FINCL5LONLAT, FWRTPR1, FWRTPR2, FWRTPR3, FWRTPR4,
FWRTPR5, FWRTPR6, HFILENAME SPEC (6), INITHIST, MFILT(6), NDENS(6), NHTFRQ(6),
PRECC THRESH, PRECL THRESH
B.5 CAMEXP mass store control namelist variables ARCHIVE DIR, MSS IRT, MSS WPASS
B.6 CAMEXP restart file namelist variables BRNCH RETAIN CASENAME, NREFRQ, NREVSN, REST PFILE
B.7 CAMEXP dynamics namelist variables DIF2, DIF4, DIVDAMPN, EPS, IORD, JORD, KMXHDC, KORD, NSPLIT, USE ETA,
B.8 CAMEXP physics namelist variables ADIABATIC, AERO CARBON, AERO FEEDBACK CARBON, AERO FEEDBACK SEA SALT, AERO SEA SALT, AQUA PLANET, BGSCL RF, CARSCL RF, CARSCL, CH4VMR, CO2VMR, DOISCCP, DUSTSCL RF, DUSTSCL, F11VMR, F12VMR, FLXAVE, ICE CONSCHK FRQ, IDEAL PHYS, INDIRECT, IRADAE, IRADLW, IRADSW, ITSST, N2OVMR, NLVDRY, PERTLIM, PRESCRIBED SULFUR, PROGNOSTIC ICESNOW, PROGNOSTIC SULFUR, RADFORCE, RAMPYEAR GHG, RAMPYEAR PRESCRIBED SULFUR, RAMPYEAR PROGNOSTIC SULFUR, RAMPYEAR SCON, RAMP CO2 ANNUAL RATE, RAMP CO2 CAP, RAMP CO2 START YMD, RESET CSIM ICE PROPS, SCENARIO CARBON SCALE, SCENARIO GHG, SCENARIO PRESCRIBED SULFUR, SCENARIO PROGNOSTIC SULFUR, SCENARIO SCON, SCON, SOM CONSCHK FRQ, SSLTSCL RF, SSLTSCL, STRAT VOLCANIC, SULSCL RF, SULSCL, TAUBACK, TAUVIS, TRACE GAS, VOLCSCL RF, VOLCSCL B.9 CAMEXP non-water constituent namelist variables NUSR ADV, NUSR NAD, READTRACE 62
B.10 CAMEXP memory namelist variables
FHSTPR1, FHSTPR2, FHSTPR3, FHSTPR4, FHSTPR5, FHSTPR6, PRINT STEP COST
LINEBUF,
NHSTPR(6),
B.11 CAMEXP performance tuning namelist variables DYN ALLGATHER, DYN ALLTOALL, FORCE 2D, GEOPKTRANS, MODCOMM GEOPK, MODCOMM TRANSPOSE, NPR YZ, OMPNEST, PHYS ALLTOALL, PHYS CHNK PER THD, PHYS LOADBALANCE, SWAP COMM ORDER, SWAP COMM PROTOCOL, TRACERTRANS
B.12 CAMEXP orbital parameter namelist variables
ECCEN, IYEAR AD, MVELP, OBLIQ
B.13 Complete list of CAM namelist variables Table B.1 displays all supported variables. Most of the variables in CAMEXP are single-valued, but some are array-valued. Included in the table are the following pieces of information: · Variable name. · Variable type (Char, Integer, Real, or Logical). If the variable is of type Char, then its declared length is displayed along with the variable type (e.g. CTITLE is 80 characters in length, therefore Char*80 is entered in the "Type" column). · Default value. · References to examples in Section 2.3 demonstrating usage. · Variable description
Name ABSEMS DATA ADIABATIC AEROPTICS
Table B.1: CAMEXP namelist variables
Type Default Ex. Description
Char*256 See
Filename of absorption/emission dataset.
Desc.
This file is a required input dataset. It consists
of terms used for determining the absorptivity
and emissivity of water vapor in the longwave
parameterization of radiation. Default is set
in DefaultCAMEXPNamelist.xml.
Logical .FALSE.
If true, do not run model physics, only run
the dynamical core. In this mode, water va-
por is advected as a passive tracer. Only
one of ADIABATIC, IDEAL PHYS, or
AQUA PLANET can be true.
Char*256 See
Full pathname of dataset for time-invariant
Desc.
aerosol optical properties. Default is set in
DefaultCAMEXPNamelist.xml.
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Name AERO CARBON AERO FEEDBACK CARBON AERO FEEDBACK SEA SALT AERO SEA SALT AQUA PLANET ARCHIVE DIR AVGFLAG PERTAPE (6) BGSCL RF BNDTVAER BNDTVCARBONSCALE BNDTVDMS
Type Default Ex. Description
Logical .FALSE.
If true, turn on carbon prognostic aerosols.
Logical .FALSE. Logical .FALSE. Logical .FALSE.
If true, turn on feedback of carbon prognostic aerosols. May only be true if AERO CARBON is also true. If true, turn on feedback of sea salt prognostic aerosols. May only be true if AERO SEA SALT is also true. If true, turn on sea salt prognostic aerosols.
Logical false Char*256 See Desc.
Char*1
See Desc.
Real
0
Char*256 See Desc. Char*256 See Desc. Char*256 See Desc.
Run model in "AQUA PLANET" mode. Only one of ADIABATIC, IDEAL PHYS, or AQUA PLANET can be true. Head mass store archival directory name. Default is /$USER/csm/caseid/ (where caseid is the caseid from the namelist and $USER is the username converted to uppercase.) CAM history files will be stored under $ARCHIVE DIR/atm/hist, restart files under $ARCHIVE DIR/atm/rest, and initial files under $ARCHIVE DIR/atm/init. Landmodel output files will be stored under similar directory names with "lnd" to specify the land-model subdirectory. Sets the averaging flag for all variables on a particular history file series. Default is to use default averaging flags for each variable Valid values are A, I, X, and M, indicating Average (A), Instantaneous (I), Maximum (X), and Minimum (M). Set background aerosol scaling factor for Radiative Forcing calculation. This does not affect mmr's used for the climate integration, and are is used when RADFORCE is true. Full pathname of time-variant boundary dataset for aerosol mass mixing ratios. Default is set in DefaultCAMEXPNamelist.xml. Full pathname of time-variant boundary dataset for carbon scaling. Default is set in DefaultCAMEXPNamelist.xml. Full pathname of time-variant boundary dataset for DMS surface emissions. This is used as an input for prognostic sulfate computations. Default is set in DefaultCAMEXPNamelist.xml.
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Name BNDTVGHG BNDTVG BNDTVOXID BNDTVO BNDTVSCON BNDTVSF6 BNDTVSOX BNDTVS BNDTVVOLC BRNCH RETAIN CASENAME CALENDAR CARSCL RF CARSCL
Type Default Ex. Description
Char*256 See
Full pathname of time-variant boundary
Desc.
dataset for greenhouse gas surface values. De-
fault is set in DefaultCAMEXPNamelist.xml.
Char*256 See Desc. Char*256 See Desc.
Full pathname of time-variant boundary dataset for greenhouse loss rates. (required if trace gas is set to true). Default is set in DefaultCAMEXPNamelist.xml. Full pathname of time-variant boundary dataset for oxidants. Default is set in DefaultCAMEXPNamelist.xml.
Char*256 See Desc. Char*256 See Desc.
Full pathname of time-variant ozone mixing ratios boundary dataset (NetCDF format). Default is set in DefaultCAMEXPNamelist.xml. Full pathname of time-variant boundary dataset for solar constant. Default is set in DefaultCAMEXPNamelist.xml.
Char*256 See Desc. Char*256 See Desc.
Full pathname of time-variant boundary dataset for tracer test emissions (required if tracers flag is set to true). Default is set in DefaultCAMEXPNamelist.xml. Full pathname of time-variant boundary dataset for SOx surface emissions. Default is set in DefaultCAMEXPNamelist.xml.
Char*256 See Desc. Char*256 See Desc. logical false
??, Full pathname of time-variant sea-surface ??, temperature and sea-ice concentration bound?? ary dataset (NetCDF format). Default is set in DefaultCAMEXPNamelist.xml. Full pathname of time-variant boundary dataset for stratospheric volcanic aerosol mass mixing ratios. Default is set in DefaultCAMEXPNamelist.xml. If TRUE, use the pre-existing case name for a branch run.
Char*32 NO LEAP
Real
0
Real
1.0
Calendar type 'NO LEAP' for consistent 365days per year or 'GREGORIAN' to include leap-years. Note that if "GREGORIAN" is selected although leap-years will be used in the calender manager the calculation of the earth's orbit still assumes 365 day years., Valid values: "NO LEAP" or "GREGORIAN" Set carbon aerosol scaling factor for radiative forcing calculation. This does not affect mmr's used for the climate integration, and is only used when RADFORCE is true. Set carbon aerosol scaling factor for radiative transfer calculations. This may be used to scale the specified or prognostic aerosol mass mixing ratios.
65
Name CASEID CH4VMR CO2VMR CO EMIS CTITLE DIF2 DIF4 DIVDAMPN DOISCCP DTIME DUSTSCL RF DUSTSCL
Type Char*32 Real
Default Ex. camrun ?? 1.714e-6 ??
Description Case identifier (saved in history file header record) and normally used as part of the MSS path name (see the ARCHIVE DIR namelist option). By default also used in output filenames (see the HFILENAME SPEC namelist option). Setting is Required. CH4 volume mixing ratio.
Real
3.550e-4 ?? CO2 volume mixing ratio
Char*256 See Desc. Char*80 None
Full pathname of time-variant boundary dataset for fossil fuel carbon surface emissions. Default is set in DefaultCAMEXPNamelist.xml. ?? Case title
Real Real Real
See Desc. See Desc. 0.0
Logical false
Real
See Desc.
Real
0
Real
1.0
del2 horizontal diffusion coefficient. Default is resolution dependent, e.g. 2.5e5 for T42 EUL. Not used for fv dynamics. del4 horizontal diffusion coefficient. Default is resolution dependent, e.g. 1.0e16 for T42 EUL. Not used for fv dynamics. Number of days (from timestep 0) to run divergence damper. Use only if model becomes dynamicallly unstable during initialization. Suggested value: 2. (Value must be >= 0.) Not used for fv dynamics. If true, the ISCCP cloud simulator will be run, and output added to the monthly history files. ?? Length of model timestep in seconds. CAUTION: Changing this variable directly impacts the physical parameterizations in the model and may impact the climate. Changing resolution usually requires a change in DTIME. Defaults are resolution-dependent, e.g 1200. for T42 EUL; 1800 for FV 2x2.5. Set dust aerosol scaling factor for radiative forcing calculation. This does not affect mmr's used for the climate integration, and is only used when RADFORCE is true. Set dust aerosol scaling factor for radiative transfer calculations. This may be used to scale the specified or prognostic aerosol mass mixing ratios.
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Name DYN ALLGATHER DYN ALLTOALL ECCEN EMPTY HTAPES EPS F11VMR F12VMR FEXCL1, FEXCL2, FEXCL3, FEXCL4, FEXCL5, FEXCL6 (200) FHSTPR1, FHSTPR2, FHSTPR3, FHSTPR4, FHSTPR5, FHSTPR6 (200) FINCL1, FINCL2, FINCL3, FINCL4, FINCL5, FINCL6 (200)
Type Default Ex. Description
Integer 0
dynamics gather option. (only used with EUL
and SLD dycores).
Integer 0
dynamics transpose option. (only used with EUL and SLD dycores).
Real
None
??
Logical .FALSE.
Real
0.06
Earth's eccentricity of orbit. (unitless: typically 0. to 0.1). Setting is Required if IYEAR AD not set. Not used when running as part of CCSM. If set don't put any of the variables on the history tapes by default. Only output the variables that the user explicitly lists in the fincl# namelist items. Time filter coefficient.
Real
0.280e-9 ?? CFC11 volume mixing ratio.
Real
0.503e-9 ?? CFC12 volume mixing ratio.
Char*8 None Char*8 None
?? List of fields to exclude on the default history files (must be in Master Field List). The default history files include a monthly series and a daily series. For a list of what fields are included on the first history file series by default see Table 3.1. Specific fields for each history file for which to use the non-default history buffer precision.
Char*8 None
??, List of fields to include on the history files. ?? The added fields must be in Master Field List see Table 3.1 for the list of fields that can be added as well as which fields are on the first history file series by default (FINCL1). Using a ":" following a field gives the averaging flag for the output field. Valid flags are: I for instantaneous, A for average, M for minimum, and X for maximum. See Section 2.5.1.1 for more information on the averaging flag.
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Name FINCL1LONLAT, FINCL2LONLAT, FINCL3LONLAT, FINCL4LONLAT, FINCL5LONLAT (200) FLXAVE FORCE 2D FWRTPR1, FWRTPR2, FWRTPR3, FWRTPR4, FWRTPR5, FWRTPR6 (200) GEOPKTRANS
Type Default Ex. Description
Char*8 None
List of columns or contiguous columns at
which the fincl1 fields will be output. Indi-
vidual columns are specified as a string using
a longitude degree (greater or equal to 0.) fol-
lowed by a single character (e)ast/(w)est iden-
tifer, an underscore ' ' , and a latitude degree
followed by a single character (n)orth/(s)outh
identifier. For example, '10e 20n' would
pick the model column closest to 10 de-
grees east longitude by 20 degrees north lat-
itude. A group of contiguous columns can
be specified using bounding latitudes and lon-
gitudes separated by a colon. For exam-
ple, '10e:20e 15n:20n' would select the model
columns which fall with in the longitude range
from 10 east to 20 east and the latitude range
from 15 north to 20 north.
Logical See
This namelist variable is only used when run-
Desc.
ning through the flux coupler. In that case,
the default value is true. If true, data is sent to
the flux coupler only on radiation time steps.
Integer 0
option to force transpose computation for 1D
decomp. (used with Finite-Volume dynamical
core only).
Char*8 None
Specific fields for each history file which will be written using the non-default precision.
Integer 0
Geopotential method (used with FiniteVolume dynamical core only).
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Name HFILENAME SPEC (6) ICE CONSCHK FRQ IDEAL PHYS INDIRECT
Type Default Ex. Description
Char*256 See
Array of history filename speci-
Desc.
fiers. Defaults are "%c.cam2.h%t.%y-
%m",
"%c.cam2.h%t.%y-%m-%d-%s",
"%c.cam2.h%t.%y-%m-%d-%s", ... File-
name, specifiers give generic formats for the
filenames with the specific dates, file-series
number, and caseid, filled in when the files are
created. The following strings are expanded
when the filename is created:
· %c = caseid
· %t = tape series number (0-5)
· %y = year (normally 4 digits, more digits if needed)
· %m = month
· %d = day
· %s = seconds into current day
· %% = % symbol
Integer 0 Logical false Logical false
For example, for a simulation with caseid="test" and current date of 0000/12/31 0:00UT, the monthly average files with a filename specifier of "%c.cam2.h%t.%y%m.nc" expand into "test.cam2.h0.000012.nc", daily files with a filename specifier of "%c.cam2.h%t.%y-%m-%d-%s.nc" expand to ""test.cam2.h0.0000-12-31-00000.nc". Spaces are not allowed in filename specifiers. Although the character "/" is allowed in the specifier, it will be interpreted as a directory name and the corresponding directories will have to be created in the model execution directory (directory given to configure with cam exedir option) before model execution. This is not used only when running as part of CCSM. If n > 0, sea ice global energy checking will be done every n timesteps. If n < 0, sea ice global energy checking will be done every n days. If true, Run ONLY the "idealized" dynamical core of the model (dynamics + Held&Suarez-specified physics). Only one of ADIABATIC, IDEAL PHYS, or AQUA PLANET can be true. If true, include the indirect radiative effects of sulfate aerosols.
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Name INITHIST IORD IRADAE IRADLW IRADSW ISCCPDATA ITSST IYEAR AD JORD KMXHDC KORD
Type Char*8 Integer
Default Ex. YEARLY 4
Description Frequency that initial files will be output: 6-hourly, daily, monthly, yearly, or never. Valid values: 'NONE', '6-HOURLY', 'DAILY', 'MONTHLY', 'YEARLY' East-west transport scheme (used with FiniteVolume dynamical core only).
Integer -12 Integer -1 Integer -1 Char*256 See Desc. Integer 1
Frequency of absorptivity/emissivity calculations in time steps (if positive) or model hours (if negative). To avoid having the abs/ems values saved on the restart output, this variable should divide evenly into MFILT(1)*NHTFRQ(1). Frequency of long-wave radiation calculation in timesteps (if positive) or model hours (if negative). Frequency of short-wave radiation calculation in timesteps (if positive) or model hours (if negative). Full pathname of time-invariant dataset used by the ISCCP cloud simulator. Default is set in DefaultCAMEXPNamelist.xml. Frequency of SST update in timesteps.
Integer 1950 Integer 4 Integer 5 Integer 4
??, Year (AD) used to compute earth's orbital pa?? rameters. If not set, then use the values from the eccen, mvelp, and obliq namelist parameters. If only IYEAR AD is set, orbital parameters will be computed automatically (based on Berger, 1977). If one of OBLIQ, ECCEN, OR MVELP is set, all three must be set. If all four of the above are set by the user, IYEAR AD takes precedence. Setting is Required unless ECCEN, OBLIQ and MVELP are set. Not used when running as part of CCSM. North-south transport scheme (used with Finite-Volume dynamical core only). Number of levels over which to apply Courant limiter, starting at top of model. Vertical mapping (used with Finite-Volume dynamical core only).
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Name LINEBUF MFILT(6) MODCOMM GEOPK MODCOMM TRANSPOSE MSS IRT MSS WPASS MVELP N2OVMR NCDATA NDENS(6) NELAPSE
Type Default Ex. Description Logical .FALSE. ?? If true, force buffer flush of stdout with each new-line generated (useful for debugging).
Integer Integer Integer Integer Char*8 Real Real
30, 30, ??, 30, ... ??, ?? 0
0
365
??,
??,
??,
??
None
??,
??
None
??
0.311e-6 ??
Array of number of time samples to write to each history files series (a time sample is the history output from a given timestep). mod comm geopk method (varies with mpi/mpi2 choice) (used with Finite-Volume dynamical core only). mod comm transpose method (varies with mpi/mpi2 choice) (used with Finite-Volume dynamical core only). Retention period in days for history and restart files stored on NCAR Mass Store. If MSS IRT=0, no history or restart files will be archived. NCAR Mass Store write password for all output datasets. Must remain the same throughout a case run, or a continuation run will not update original history files. Earth's moving vernal equinox at perihelion (degrees: 0. to 360.0). Setting is Required if IYEAR AD not set. Not used when running as part of CCSM. N2O volume mixing ratio.
Char*256 See Desc. Integer 2, 2, 2, ... Integer None
??, Full pathname of initial atmospheric state ?? dataset (NetCDF format). See Section 2.5.1 for details. Default is set in DefaultCAMEXPNamelist.xml. ??, Array specifying output format for each his??, tory file series. Valid values are 1 or 2. "1" ?? implies output to be written out in 64-bit NetCDF format, and "2" writes data out in 32-bit NetCDF format. Elapsed time to run. In time steps (positive) or days (negative) to run. May be entered instead of NESTEP or STOP YMD and STOP TOD. Note, NESTEP is not required or used when running as part of CCSM. Setting is Required if NESTEP or STOP YMD not set.
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Name NESTEP NHSTPR(6) NHTFRQ(6) NLVDRY NPR YZ NREFRQ NREVSN NSPLIT NSREST NUSR ADV
Type Default Ex. Description
Integer None
Ending timestep. If positive the ending ab-
solute timestep (from the start of the ini-
tial run). If negative the ending abso-
lute number of days to process (from the
start of the initial run). Either NELAPSE,
NESTEP or (STOP YMD,STOP TOD) must be
set if not running through flux coupler.
(STOP YMD,STOP TOD) take precedence if set.
Note, NESTEP is not required or used when
running as part of CCSM. Setting is Re-
quired if NELAPSE and STOP YMD not set.
Real
8, 8,
Default history buffer precision (8 or 4 bytes)
8, ...
for each history file.
Integer 0, -24, ??, Array of write frequencies for each history
-24,
??, files series. If NHTFRQ(1)=0, the file will be
-24,
?? a monthly average. Only the first file series
...
may be a monthly average. If NHTFRQ(i)>0,
frequency is input as number of timesteps. If
NHTFRQ(i)<0, frequency is input as number
of hours. Note that NHTRFQ(1) also con-
trols the frequency of restart dataset writes if
NREFRQ = 1.
Integer 3
Number of layers from the top of the model
over which to do dry convective adjustment.
Must be less than plev (the number of vertical
levels).
Integer 0, 0,
YZ and XY decompositions (used with Finite-
0, 0
Volume dynamical core only).
Integer 1 Char*256 None Integer 0 Integer 0 Integer 0
Controls whether restart datasets are written. This variable can only be 1 or 0. If 1, restart files are written and archived for every archive of the first history file series. If this variable is 0, then no restarts are written. Full pathname of master restart file from which to branch. Setting is Required for branch run. Lagrangian time splits when using FiniteVolume dynamics. If zero, a best-estimate will be automatically calculated. ??, Run type: 0=initial , 1=restart , 3=branch ??, ?? number of user defined advected tracers
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Name NUSR NAD OBLIQ OMPNEST OZNCYC PERPETUAL RUN PERPETUAL YMD PERTLIM PHYS ALLTOALL PHYS CHNK PER THD PHYS LOADBALANCE PRECC THRESH PRECL THRESH PRESCRIBED SULFUR
Type Default Ex. Description
Integer 0
number of user defined non-advected tracers
Real
None
Integer 0
?? Earth's orbital angle of obliquity (degrees: 90. to +90., typically 22. to 26.). Setting is Required if IYEAR AD not set. Not used when running as part of CCSM. Option for nested openmp (used with FiniteVolume dynamical core only).
Logical .TRUE.
Logical false Logical false
Real
0.0
Integer 0
Flag for yearly cycling of ozone data. If set to .FALSE., a multi-year dataset is assumed, otherwise a single-year dataset is assumed, and ozone will be cycled over the first 12 values in the file. Set to .true. to specify that the run will use a perpetual calendar. If perpetual ymd is not set then the perpetual date will be read from the initial file. Perpetual date specified as (year*1000 + month*100 + day). This date overrides the date from the initial file. If aqua planet=.true. then perpetual ymd is ignored and the perpetual date is set to 321. Perturb the initial conditions for temperature randomly by up to the given amount. Only applied for initial simulations. Dynamics/physics transpose option.
Integer 1
Integer 0
Real
0.1 mm/hr
Real
0.05 mm/hr
char*16 direct
Select target number of chunks per thread. Must be positive Select different options for organization of physics chunks. Each uses a different scheme for static load balancing. Precipitation threshhold for use with the PRECCINT and PRECCFRQ fields for history files. Precipitation threshhold for use with the PRECLINT and PRECLFRQ fields for history files. Control radiative interaction of prescribed sulfur. May be set to "passive" or "direct". passive = prescribed sulfur has no radiative interaction direct = prescribed sulfur drives radiative interaction
73
Name PRINT STEP COST
Type Default Ex. Description
Logical .FALSE.
If true, print CPU timing per model timestep.
PROGNOSTIC ICESNOW PROGNOSTIC SULFUR RADFORCE
Logical .TRUE. char*16 off Logical false
Accumulate snow over sea-ice (with a 0.5m maximum). If .FALSE. then use a climatology for snow depth. Control prognostic sulfur calculations. May be set to "off", "passive", or "direct". off = no prognostic sulfur (default) passive = prognostic sulfur computed with no radiative interaction direct = prognostic sulfur computed and drives radiative interaction Compute forcing from aerosols
RAMPYEAR GHG
integer 0
integer none RAMPYEAR PRESCRIBED SULFUR
Ramped gases fixed at this year if set to a value greater than zero. Only used if SCENARIO GHG is set to RAMPED. This variable is reserved for future use. No value is permitted.
integer none RAMPYEAR PROGNOSTIC SULFUR
Set to YYYY in order to cycle that year of sox emissions.
RAMPYEAR SCON RAMP CO2 ANNUAL RATE
integer 0
real
1.0
Ramped scon fixed at this year if set to a value greater than zero. Only used if SCENARIO SCON is set to RAMPED. percentage amount of co2 ramping per year
RAMP CO2 CAP RAMP CO2 START YMD READTRACE REF TOD
real
See Desc.
integer 0
Logical .TRUE.
Integer See Desc.
co2 cap if rate > 0, floor otherwise; specified as multiple or fraction of inital value; e.g. setting to 4.0 will cap at 4x initial co2 setting; default is boundless if rate > 0, zero otherwise date on which ramping of co2 begins; REQUIRED to be set for scenario ghg='RAMP CO2 ONLY' If true, initialize data for all consituents found on the initial conditions dataset. Otherwise data will be initialized using internallyspecified default values. Reference time-of-day (seconds). Default is to use starting time of day
74
Name REF YMD RESET CSIM ICE PROPS REST PFILE
Type Default Ex. Description
Integer
Reference date for run as yyyymmdd. Default
is to use starting date. The reference date is
the reference for the time variable output on
the history files.
Logical .FALSE.
Reset the CSIM ice-model properties. Snow-
cover is set to zero, and ice-temperatures are
all set to freezing. This is important when
starting from an initial dataset that isn't in
equilibrium. This is used, for example, when
starting from initial conditions that are inter-
polated from a different resolution.
Char*256 See
Full pathname of restart pointer file. Default
Desc.
is $HOME/ cam2.CASEID.rpointer
SCENARIO CARBON SCALE
char*16 FIXED
SCENARIO GHG
char*16 FIXED
char*16 FIXED SCENARIO PRESCRIBED SULFUR
Controls carbon scaling. May be set to 'FIXED' or 'RAMPED'. FIXED means use the value specified by CARSCL. RAMPED means use data from file specified by BNDTVCARBONSCALE. Controls treatment of specified co2,ch4,n2o,cfcf11,cfc12 volume mixing ratios. May be set to 'FIXED' or 'RAMPED' or 'RAMP CO2 ONLY'. FIXED = volume mixing ratios are fixed and have either default or namelist input values RAMPED = volume mixing ratios are ramped RAMP CO2 ONLY = only co2 mixing ratios are ramped Controls prescribed sulfur amounts. Can only be set to 'FIXED' ! FIXED = uses climatology
char*16 RAMPED SCENARIO PROGNOSTIC SULFUR
SCENARIO SCON SCON
char*16 FIXED
Real
1.367E6 ??
Sets so2 and so4 surface fluxes. May only be set to 'RAMPED' ! RAMPED = uses boundary data set bndtvsox. Only used if PROGNOSTIC SULFUR is set to PASSIVE or DIRECT. Controls the solar constant. Can be set to 'FIXED' or 'RAMPED'. FIXED = scon is fixed and can have either the default or namelist value. RAMPED = scon is ramped. Solar constant (W/m2).
SOIL EROD SOM CONSCHK FRQ
Char*256 See Desc. Integer 0
Full pathname of time-variant boundary dataset for soil erodibility factors. Default is set in DefaultCAMEXPNamelist.xml. This is used only when running with the slab ocean model. If n > 0, SOM global energy checking will be done every n timesteps. If n < 0, SOM global energy checking will be done every n days.
75
Name SSLTSCL RF SSLTSCL SSTCYC START TOD START YMD STOP TOD STOP YMD STRAT VOLCANIC SULSCL RF SULSCL SWAP COMM ORDER SWAP COMM PROTOCOL
Type Default Ex. Description
Real
0
Set sea salt aerosol scaling factor for radia-
tive forcing calculation. This does not affect
mmr's used for the climate integration, and is
only used when RADFORCE is true.
Real
1.0
Set sea salt aerosol scaling factor for radia-
tive transfer calculations. This may be used to
scale the specified or prognostic aerosol mass
mixing ratios.
Logical .TRUE. ?? Flag for yearly cycling of SST data. If set
to .FALSE., a multi-year dataset is assumed,
otherwise a single-year dataset is assumed,
and SSTs will be cycled over the first 12 val-
ues in the file. Not used if running with
CCSM.
Integer See
Starting time-of-day (seconds). Default is to
Desc.
use time of day from initial condition dataset.
If not input, value is set to NCSEC from initial
dataset header.
Integer See
Starting date for run as yyyymmdd. Default is
Desc.
to Use date from initial condition dataset. If
not input, value is set to NCDATE from initial
dataset header.
Integer 0
Stopping time of day for run in seconds since
0Z. Not used when running through flux cou-
pler.
Integer None Logical false
Stopping date for run encoded in yearmmdd format. Either NELAPSE, NESTEP or STOP YMD (and possibly STOP TOD) must be set if not running through flux coupler. (STOP YMD,STOP TOD) takes precedence if set. STOP YMD is not required or used when running as part of CCSM. Setting is Required if NELAPSE and NESTEP not set. Use stratospheric volcanic aerosols masses and couple with radiative forcing computations.
Real
0
Real
1.0
Integer 0 Integer 0
Set sulfur aerosol scaling factor for radiative forcing calculation. This does not affect mmr's used for the climate integration, and is only used when RADFORCE is true. Set sulfur aerosol scaling factor for radiative transfer calculations. This may be used to scale the specified or prognostic aerosol mass mixing ratios. Performance tuning option for swap communication. (only used with EUL and SLD dycores). Performance tuning option for swap communication. (only used with EUL and SLD dycores).
76
Name TAUBACK TAUVIS TRACERTRANS TRACE GAS USE ETA VOLCSCL RF VOLCSCL
Type Real Real
Default Ex. Description
0.0
Optical depth of (rh = 0.8, sulfate-like) back-
ground aerosol.
0.14
Visible optical depth.
Integer 0 Logical false Logical .FALSE.
Real
0
Real
1.0
Number of simultaneously transposed tracers (used with Finite-Volume dynamical core only). If true, turn on prognostic greenhouse gas calculations for CH4, N2O, CFC11 and CFC12. This requires adding the option "-nadv 7" when running configuration. If TRUE, use the vertical coordinate (eta) values defined in the finite volume dynamical core code rather than the values defined on the input dataset (used with Finite-Volume dynamical core only). Set volcanic aerosol scaling factor for radiative forcing calculation. This does not affect mmr's used for the climate integration, and is only used when RADFORCE is true. Set volcanic aerosol scaling factor for radiative transfer calculations. This may be used to scale the specified or prognostic aerosol mass mixing ratios.
77
78
Appendix C CLM namelist variables
This appendix describes a small subset of the namelist variables recognized by CLM 3.0. For more information, please see the CLM User's Guide. A CAM model run is controlled using the build-namelist facility described in Section 2.2. The focus of this appendix is to provide a reference for select CLM variables that may be set through the use of build-namelist's -namelist option.
Table C.1: CLMEXP namelist variables
Name FINIDAT FPTFTCON FSURDAT MKSRF FVEGTYP MKSRF FSOITEX
Type Default Ex. Description
Char*256 None
Initial dataset of the land surface model state (ini-
tial temperatures, soil water content etcetera). If
this dataset is not provided the model will use
reasonable values to start from. Note, that some
features of the land-surface model take several
simulation years to "spin-up" before they reach
equilibrium.
Char*256 None
Dataset of plant-function types. Setting is Re-
quired
Char*256 None
Time invariant surface dataset for this resolution.
If this dataset is not provided on an initial run
the high resolution datasets MKSRF FVEGTYP,
MKSRF FSOITEX, MKSRF FSOICOL, MK-
SRF FLANWAT, MKSRF FURBAN, MK-
SRF FGLACIER, and MKSRF FLAI must be
provided, and will be used to create the surface
dataset. On a continuation run (branch or
restart) this dataset MUST be provided.
Char*256 None
High resolution Vegetation Type dataset needed
to determine the time-invariant surface dataset
(FSURDAT). (Required if FSURDAT not de-
fined)
Char*256 None
High resolution Soil Texture dataset needed
to determine the time-invariant surface dataset
(FSURDAT). (Required if FSURDAT not de-
fined)
79
Name
Type Default Ex. Description
MKSRF FSOICOL Char*256 None
High resolution Soil Color dataset needed to
determine the time-invariant surface dataset
(FSURDAT). (Required if FSURDAT not de-
fined)
MKSRF FLANWAT Char*256 None
High resolution Land water (lake and river)
dataset needed to determine the time-invariant
surface dataset (FSURDAT). (Required if FSUR-
DAT not defined)
MKSRF FURBANP Char*256 None
High resolution Urban Area dataset needed
to determine the time-invariant surface dataset
(FSURDAT). (Required if FSURDAT not de-
fined)
MKSRF FGLACIER Char*256 None
High resolution Glacier dataset needed to deter-
mine the time-invariant surface dataset (FSUR-
DAT). (Required if FSURDAT not defined)
MKSRF FLAI
Char*256 None
High resolution Leaf Area Index (LAI) dataset
needed to determine the time-invariant surface
dataset (FSURDAT). (Required if FSURDAT not
defined)
80
Appendix D Details of the configuration files The configure utility creates the header files misc.h, params.h, and preproc.h and the directory search path file Filepath. These files are written to the directory given by the -cam bld argument of configure (the default is the directory from which configure is executed). It is not necessary to edit these files to produce supported CAM configurations as that can be easily accomplished by the configure utility. However, a user experimenting with non-standard configurations may need to edit these files directly. Thus, the file contents are summarized below. D.1 Filepath Contains a list of directories used by gmake to determine the list of source files to build. All source files listed by the filename expansion expressions *.F90, *.F, and *.c in each of the directories are included in the build. It a given filename occurs in more than one of the directories, it is the version in the first directory of the list that will be built. The list of directories in Filepath will vary with target architecture and depend on the specified dynamics and physics packages. D.2 misc.h Contains a list of resolution-independent cpp directives. The following cpp tokens must either be defined or undefined (i.e. preceded by #define or #undef). D.3 params.h Contains a list of resolution-dependent cpp directives for the atmosphere model. D.4 preproc.h Contains a list of resolution-dependent cpp tokens for the land-model code. Currently the resolution of the land-model must be the same as that of the atmospheric component. 81
token COUP CSM PERGRO USEFFTLIB SPMD STAGGERED
Table D.1: misc.h pre-processor tokens Synopsis Define if the flux-coupled ocean configuration will be used. COUP CSM is always undefined for stand-alone mode. Define if you want to make error growth tests with your model simulation. This token turns off parts of the prognostic cloud water parameterization so that the error growth happens at a reasonable rate. Default setting is with PERGRO undefined. Define if you want to use a intrinsic FFT package rather than the ECMWF FFT package provided with the code in the "models/atm/cam/src/utils" directory. Default setting is USEFFTLIB undefined. Enables the distributed memory (SPMD) implementation. Enables staggered grid processing. Required for use with the Lin-Rood dynamical core, otherwise undefined.
D.5 config cache.xml Not yet described.
D.6 Makefile Not yet described.
82
token PCNST PNATS PLEV PLEVR PLON PLAT PCOLS PTRM PTRN PTRK
Table D.2: params.h pre-processor tokens Synopsis Number of advected constituents including water vapor and cloud-water. Default setting is 1 (for water vapor). Number of non-advected constituents. Default setting is 1 (for cloud water). Number of vertical levels. Default setting is 26. Number of vertical levels over which radiation calculations are performed. Use of separate vertical coordinate for the radiation calculation has not been tested. Therefore this directive must currently be set to the same value as PLEV. Number of longitudes on the transform grid. Default setting is 128. Number of Gaussian latitudes on the CAM2.0 transform grid. Default setting is 64. Maximum number of columns to use for the physics. This value can be tuned for different computer architectures in order to increase performance. Default setting is 16. Spectral truncation of the zonal wavenumber m. Default setting is 42. Spectral truncation of the total wavenumber n for zonal wavenumber 0. Default setting is 42. Maximum total wavenumber k, for any zonal wavenumber m. Default setting is 42.
token COUP CAM LSMLON LSMLAT
Table D.3: preproc.h pre-processor tokens Synopsis Tell the CLM that it is being run as a subroutine beneath the atmospheric model. Number of longitudes for the landmodel grid. Currently this directive must have the same value as PLON in params.h. Number of latitudes for the land-model grid. Currently this directive must have the same value as PLAT in params.h. 83
84
Bibliography Collins, W. D., P. J. Rasch, and Others, Description of the NCAR Community Atmosphere Model (CAM 3.0), Technical Report NCAR/TN-464+STR, National Center for Atmospheric Research, Boulder, Colorado, 210 pp., 2004. 85

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