sdiff -s  suppress all common lines
< cesm_doc                                                    cesm_doc_test104 > 
 
========================== app1.xml =================================
 
 
========================== app2.xml =================================
 
 
========================== app3.xml =================================
 
 
========================== app4.xml =================================
 
 
========================== app5.xml =================================
 
 
========================== app6.xml =================================
 
 
========================== app7.xml =================================
 
 
========================== app8.xml =================================
 
 
========================== bookinfo.xml =================================
<title>CESM1.0.3 User's Guide </title>					  |	<title>CESM1.0 User's Guide </title>
 
 
========================== chap1.xml =================================
<para> <ulink url="http://www.unidata.ucar.edu/software/netcdf/"> netc	  |	<para> <ulink url="http://http://www.unidata.ucar.edu/software/netcdf/
<para> <ulink url="http://www.earthsystemmodeling.org/download/release	  |	<para> <ulink url="http://www.earthsystemmodeling.org/index.shtml">ESM
									  >	</para>
 
 
========================== chap2.xml =================================
directory of your CESM source code. First use the -h option to		  |	directory of your ccsm source code. First use the -h option to
As explained in <link linkend="ccsm_component_sets">cesm		  |	As explained in <link linkend="ccsm_component_sets">ccsm
> create_newcase -case ~/cesm/b40.B2000 \				  |	> create_newcase -case ~/cesm1/b40.B2000 \
<filename>~/cesm/b40.B2000</filename> where $&CASE; is b40.B2000 with	  |	<filename>~/cesm1/b40.B2000</filename> where $&CASE; is b40.B2000 with
<filename>~/cesm/b40.B2000/</filename>. (Note that user-modifiable	  |	<filename>~/cesm1/b40.B2000/</filename>. (Note that user-modifiable
done using the &xmlchange; script in the $&CASEROOT;			  |	done using the <command>xmlchange</command> script in the $&CASEROOT;
changing values in the xml files. To invoke the &xmlchange; script:	  |	changing values in the xml files. To invoke the xmlchange script:
xmlchange -file [name] -id [name] -val [name] -help -silent -verbose -	  |	xmlchange -file [name] -id [name] -val [name] -help -silent -verbose -
<varlistentry><term><option>-warn</option></term>			  <
<listitem>								  <
<para>									  <
Warn and abort if you would be overwriting a current value in the fiel	  <
is useful so you make sure you aren't overwriting a field that is curr	  <
</para>									  <
</listitem>								  <
</varlistentry>								  <
									  <
<varlistentry><term><option>-append</option></term>			  <
<listitem>								  <
<para>									  <
Append the given value to the end of the current value of the field. S	  <
want to add an option to the end of an existing field, making sure you	  <
current value there (such as adding additional options to the CAM_CONF	  <
variable).								  <
</para>									  <
</listitem>								  <
</varlistentry>								  <
 
 
========================== chap3.xml =================================
CLM_QIAN, CLM1PT, and CPLHIST3HrWx. The default is CORE2_NYF.</para> <	  |	CLM_QIAN, CLM1PT. The default is CORE2_NYF.</para> <para>CORE2_NYF
observational data for forcing CLM in I compsets. CPLHIST3HrWx is to r	  |	observational data for forcing CLM in I compsets.</para>
with coupler history forcing from a previous simulation.</para>		  <
									  <
<varlistentry>								  <
<term>DATM_CPL_CASE</term>						  <
<listitem>								  <
<para> For CPLHIST3HrWx DATM_MODE only, the I_1850_SPINUP_3HrWx_CN com	  <
This is the casename to use for coupler history forcing of DATM.	  <
Default case is b40.20th.track1.1deg.012 a 20th-Century transient case	  <
otherwise UNSET.</para>							  <
</listitem>								  <
</varlistentry>								  <
									  <
<varlistentry>								  <
<term>DATM_CPL_YR_ALIGN</term>						  <
<listitem>								  <
<para> For CPLHIST3HrWx DATM_MODE only, the I_1850_SPINUP_3HrWx_CN com	  <
Year align (simulation year corresponding to starting year) for CPL hi	  <
Default is 1, for CPLHIST3HrWx compset otherwise -999 (unused).</para>	  <
</listitem>								  <
</varlistentry>								  <
									  <
<varlistentry>								  <
<term>DATM_CPL_YR_START</term>						  <
<listitem>								  <
<para> For CPLHIST3HrWx DATM_MODE only, the I_1850_SPINUP_3HrWx_CN com	  <
Starting year to loop CPL history data over.				  <
Default is 1850, for CPLHIST3HrWx compset otherwise -999 (unused).</pa	  <
</listitem>								  <
</varlistentry>								  <
									  <
<varlistentry>								  <
<term>DATM_CPL_YR_END</term>						  <
<listitem>								  <
<para> For CPLHIST3HrWx DATM_MODE only, the I_1850_SPINUP_3HrWx_CN com	  <
Ending year to loop CPL history data over.				  <
Default is 1950, for CPLHIST3HrWx compset otherwise -999 (unused).</pa	  <
</listitem>								  <
</varlistentry>								  <
									  <
url="http://www.cesm.ucar.edu/models/cesm1.0/data8/data8_doc/book1.htm	  |	url="http://www.cesm.ucar.edu/models/cesm1.0/data8/book1.html">Data
 
 
========================== chap4.xml =================================
 
 
========================== chap5a.xml =================================
 
 
========================== chap5.xml =================================
true for CESM. It is strongly recommended that a user perform a		  |	true for CESM1. It is strongly recommended that a user perform a
CESM has significant flexibility with respect to the layout of		  |	CESM1 has significant flexibility with respect to the layout of
independently in CESM, each with a unique MPI communicator. In		  |	independently in CESM1, each with a unique MPI communicator. In
The first section in the timing output, CESM TIMING PROFILE,		  |	The first section in the timing output, CCSM TIMING PROFILE,
In general, there are only a few reasonable concurrency options for CE	  |	In general, there are only a few reasonable concurrency options for CE
 
 
========================== chap6.xml =================================
<title>Porting CESM</title>						  |	<title>Porting CCSM</title>
getting the CESM model running on their local machine.  This section	  |	getting the CESM1 model running on their local machine.  This section
faster.  But eventually, users will want to setup the CESM 		  |	faster.  But eventually, users will want to setup the CESM1 
> cd ccsm4/scripts							  |	> cd cesm1/scripts
While CESM supports use of pnetcdf in pio, it's generally best to igno	  |	While CCSM supports use of pnetcdf in pio, it's generally best to igno
Basically, files in ccsm4/scripts/ccsm_utils/Machines will be added or	  |	Basically, files in cesm1/scripts/ccsm_utils/Machines will be added or
Edit ccsm4/scripts/ccsm_utils/Machines/config_machines.xml.  Add an en	  |	Edit cesm1/scripts/ccsm_utils/Machines/config_machines.xml.  Add an en
Copy the env_mach_specific file from the test1 case directory to ccsm4	  |	Copy the env_mach_specific file from the test1 case directory to cesm1
> cd ccsm4/scripts/test1						  |	> cd cesm1/scripts/test1
Copy the Macros file from the test1 case directory to ccsm4/scripts/cc	  |	Copy the Macros file from the test1 case directory to cesm1/scripts/cc
> cd ccsm4/scripts/test1						  |	> cd cesm1/scripts/test1
Then edit the ccsm4/scripts/ccsm_utils/Machines/Macros.bugsbunny file 	  |	Then edit the cesm1/scripts/ccsm_utils/Machines/Macros.bugsbunny file 
Create a mkbatch.bugsbunny file in ccsm4/scripts/ccsm_utils/Machines. 	  |	Create a mkbatch.bugsbunny file in cesm1/scripts/ccsm_utils/Machines. 
> cd ccsm4/scripts/ccsm_utils/Machines					  |	> cd cesm1/scripts/ccsm_utils/Machines
> cd ccsm4/scripts							  |	> cd cesm1/scripts
the new machine to the CESM scripts directly and then to test and	  |	the new machine to the CESM1 scripts directly and then to test and
Files in ccsm4/scripts/ccsm_utils/Machines will be added or modified	  |	Files in cesm1/scripts/ccsm_utils/Machines will be added or modified
> cd ccsm4/scripts							  |	> cd cesm1/scripts
Edit ccsm4/scripts/ccsm_utils/Machines/config_machines.xml.  Add an en	  |	Edit cesm1/scripts/ccsm_utils/Machines/config_machines.xml.  Add an en
> cd ccsm4/scripts/ccsm_utils/Machines					  |	> cd cesm1/scripts/ccsm_utils/Machines
> cd ccsm4/scripts/ccsm_utils/Machines					  |	> cd cesm1/scripts/ccsm_utils/Machines
While CESM supports use of pnetcdf in pio, it's generally best to igno	  |	While CCSM supports use of pnetcdf in pio, it's generally best to igno
> cd ccsm4/scripts/ccsm_utils/Machines					  |	> cd cesm1/scripts/ccsm_utils/Machines
probably be made in both the machine files in ccsm4/scripts/ccsm_utils	  |	probably be made in both the machine files in cesm1/scripts/ccsm_utils
> cd ccsm4/scripts							  |	> cd cesm1/scripts
Follow the <ulink url="http://www.cesm.ucar.edu/models/cesm1.0/cice/va	  |	Follow the <ulink url="http://www.cesm.ucar.edu/models/cesm1.0/cice/va
Follow the <ulink url="http://www.cesm.ucar.edu/models/cesm1.0/pop2/va	  |	Follow the <ulink url="http://www.cesm.ucar.edu/models/cesm1.0/pop2/va
CESM diagnostics </ulink>).  Model output data for these runs will	  |	CESM1.0 diagnostics </ulink>).  Model output data for these runs will
 
 
========================== chap7.xml =================================
<title>CESM Testing</title>						  |	<title>CCSM Testing</title>
CESM has a few tools that support automated testing of the model.	  |	CESM1 has a few tools that support automated testing of the model.
fixed and defined within the CESM scripts.  To see the list of test ca	  |	fixed and defined within the CCSM scripts.  To see the list of test ca
be rerun (i.e. using -testid t02).  Some things to note about CESM tes	  |	be rerun (i.e. using -testid t02).  Some things to note about CCSM tes
library is part of the CESM release and is invoked by setting the 	  |	library is part of the CCSM release and is invoked by setting the 
 
 
========================== chap8.xml =================================
> hsi "cd /CCSM/csm/b40.B2000/rest/0001-02-01-00000; get *" 		  |	> msrcp "mss:/CCSM/csm/b40.B2000/rest/0001-02-01-00000/*" .
<title>Use of an Earth System Modeling Framework (ESMF) library and ES	  |	<title>Use of an ESMF library and ESMF interfaces</title>
									  >	In addition, when using the ESMF component interface, if ESMF is compi
									  >	</para>
In addition, when using the ESMF component interface, if ESMF is	  |	<para>
compiled with the Xerces XML library, CESM will automatically generate	  |	( http://www.earthsystemmodeling.org/esmf_releases/non_public/ESMF_5_2
a metadata file using the ESMF attribute capabilities; this XML		  <
metadata file provides CIM (Common Information Model) compliant		  <
documentation of CESM and the model components.  After a CESM case job	  <
is completed, a file named, CESM_Component.xml, can be found within	  <
the run directory.  For more details on ESMF Attributes and the		  <
generated XML file, refer to the <ulink					  <
url="http://www.earthsystemmodeling.org/esmf_releases/non_public/ESMF_	  <
ESMF Reference Manual section on the Attribute class </ulink>. For	  <
details on the CIM, visit the <ulink					  <
url="http://metaforclimate.eu/">European Union's METAFOR project	  <
site</ulink>.								  <
The ESMF implementation in CESM1 requires ESMF version 5.2.0p1. 	  |	The ESMF implementation in CESM1 requires at least ESMF version 5.2.0.
ESMF is NOT required or provided by CESM1. It must be downloaded and	  |	ESMF is NOT required or provided by CESM1. It must be downloaded and i
installed separately. It is safest to compile ESMF and CESM with	  <
identical compilers and mpi versions. It may be possible to use		  <
versions that are different but compatible; however, it is hard to	  <
predict which versions will be compatible and using different versions	  <
can result in problems that are difficult to track down.  In addition,	  <
depending on whether or not you wish to generate XML metadata files	  <
using the ESMF attribute functionality, you may also need to download	  <
and install the Apache Xerces C++ library; details on using the Xerces	  <
library with ESMF are described later in this document.			  <
</para>									  <
  - set ESMF_LIBDIR to a valid installation directory of ESMF version 	  |	  - set ESMF_LIBDIR to a valid installation directory of ESMF version 
  - set ESMF_LIBDIR to a valid installation directory of ESMF version 	  |	  - set ESMF_LIBDIR to a valid installation directory of ESMF version 
</listitem>								  |
</orderedlist>								  <
									  <
<para>  Set ESMF_XERCES_INCLUDE to the Xerces include directory </para	  |	<para>  Set ESMF_XERCES_INCLUDE to the xercesc include directory </par
									  >	</para>
If these environment variables are not set when ESMF is compiled, and	  |	If these environment variables are not set when ESMF is compiled, and 
CESM is run using the ESMF component interface, error messages will be	  <
written to the PET log files indicating that the Xerces library is not	  <
available.  The CESM run will continue un-hindered, however an XML	  <
metadata file will not be generated.					  <
For more detailed instructions on compiling ESMF with the Xerces	  |	For more detailed instructions on compiling ESMF with the Xerces libra
library, see the <ulink							  |	( http://www.earthsystemmodeling.org/esmf_releases/non_public/ESMF_5_2
url="http://www.earthsystemmodeling.org/esmf_releases/non_public/ESMF_	  <
User's Guide section on Building and Installing ESMF and the Xerces	  <
third-party library </ulink>.						  <
To verify the correctness of the ESMF component interfaces in CESM,	  |	To verify the correctness of the ESMF component interfaces in CESM, co
compute and compare CESM global integrals with identical runs		  <
differing only in the use of the MCT based and ESMF component		  <
interfaces. In both cases, the ESMF library should be active to		  <
guarantee identical time manager values. In both runs, the 'INFO_DBUG'	  <
parameter in env_run.xml should be set to 2 which activates the global	  <
integral diagnostics. A valid comparison would be a 10 day test from	  <
the same initial conditions. The global integrals produced in the cpl	  <
log file should be identical in both cases. This test can be setup	  <
manually as described above or a CME test can be carried out which is	  <
designed to test this exact capability.					  <
									  <
<para> The following table contains combinations of CESM/ESMF release 	  <
</para>									  <
<table  id='recommended_software_table_ESMF'><title>Recommmended Softw	  <
<tgroup cols="2">							  <
<thead>									  <
<row>									  <
<entry>CESM Version</entry>						  <
<entry>ESMF Version</entry>						  <
</row>									  <
</thead>								  <
<tbody>									  <
<row>									  <
<entry>1.0</entry>							  <
<entry>4_0_0rp2</entry>							  <
</row>									  <
<row>									  <
<entry>1.0.3</entry>							  <
<entry>5_2_0p1</entry>							  <
</row>									  <
</tbody>								  <
</tgroup>								  <
</table>								  <
									  <
 
 
========================== chap9.xml =================================
CESM recommends using the &xmlchange; tool to modify env variables.  T	  |	CESM recommends using the xmlchange tool to modify env variables.  Thi
silently with certain xml format errors.  To use &xmlchange;, do, for 	  |	silently with certain xml format errors.  To use xmlchange, do, for in
to the specified values. The "-warn" option to &xmlchange; also makes 	  |	to the specified values.
overwriting a current value in a field. And the "-append" option to &x	  <
the current value in a field and just appends a new value on the end. 	  <
be useful to know the value was merely appended and the previous value	  <
inadvertently changed as well.						  <
CESM recommends using the &xmlchange; tool to modify env variables.  &	  |	CESM recommends using the xmlchange tool to modify env variables.  xml
supports error checking as part of the implementation.  Also, using &x	  |	supports error checking as part of the implementation.  Also, using xm
silently with certain xml format errors.  To use &xmlchange;, do, for 	  |	silently with certain xml format errors.  To use xmlchange, do, for in
to the specified values. Use the "-warn" option to warn you so you don	  |	to the specified values.
a field that currently has a value. And use the "-append" option to pe	  <
current field and add a new bit on the end of it.			  <
in the CESM scripts and cases can be created with it.			  |	in the CCSM scripts and cases can be created with it.
<title>How do I add a new component model to CESM? </title>		  |	<title>How do I add a new component model to CESM1? </title>
into the CESM scripts.  To add a new component model, specifically a n	  |	into the CESM1 scripts.  To add a new component model, specifically a 
land model that is going to be added to CESM.  There are two major par	  |	land model that is going to be added to CCSM.  There are two major par
For the new component to run under the CESM driver, a new top level *_	  |	For the new component to run under the CCSM driver, a new top level *_
 
 
========================== compsets_list.xml =================================
<entry morerows="1" valign="middle">F_1850_chem (F1850C)</entry>	  <
<entry>Components: cam,clm,cice,docn,sglc</entry>			  <
</row>									  <
<row>									  <
<entry>Description: Pre-industrial cam/clm with prescribed ice/ocn</en	  <
</row>									  <
<row> 									  <
<entry morerows="1" valign="middle">F_2000_chem (F2000C)</entry>	  <
<entry>Components: cam,clm,cice,docn,sglc</entry>			  <
</row>									  <
<row>									  <
<entry>Description: Stand-alone cam default, prescribed ocn/ice</entry	  <
</row>									  <
<row> 									  <
 
 
========================== env_build_list.xml =================================
 
 
========================== env_case_list.xml =================================
 
 
========================== env_conf_list.xml =================================
 
 
========================== env_mach_pes_list.xml =================================
 
 
========================== env_run_list.xml =================================
 
 
========================== glossary.xml =================================
Refers to static input data for the model. CCSM4 input data are		  |	Refers to static input data for the model. CESM1 input data are
A supported version of CCSM4.						  |	A supported version of CESM1.
A version of CCSM4. Note: A tag may not be supported.			  |	A version of CESM1. Note: A tag may not be supported.
 
 
========================== grids_list.xml =================================
 
 
========================== machines_list.xml =================================
 <entry>INVALID: hopper is no longer valid, please use hopp2</entry>	  <
 </row>									  <
 <row>									  <
 <entry>hopp2</entry>							  <
 <entry>jaguar</entry>							  |	 <entry>janus</entry>
 <entry>ORNL XT4, os is CNL, 4 pes/node, batch system is PBS</entry>	  |	 <entry>CU Linux Cluster (intel), 2 pes/node, batch system is PBS</ent
 <entry>jaguarpf</entry>						  |	 <entry>titan</entry>
 <entry>ORNL XT5, os is CNL, 12 pes/node, batch system is PBS</entry>	  |	 <entry>ORNL XK6, os is CNL, 16 pes/node, batch system is PBS</entry>
 <entry>midnight</entry>						  |	 <entry>olympus_pgi</entry>
 <entry>ARSC Sun Cluster, os is Linux (pgi), batch system is PBS</entr	  |	 <entry>PNL cluster, os is Linux (pgi), batch system is SLURM</entry>
									  >	 </row>
									  >	 <row>
									  >	 <entry>olympus_intel</entry>
									  >	 <entry>PNL cluster, os is Linux (pgi), batch system is SLURM</entry>
 <entry>prototype_columbia</entry>					  <
 <entry>NASA Ames Linux Cluster, Linux (ia64), 2 pes/node, batch syste	  <
 </row>									  <
 <row>									  <
 
 
========================== ug.xml =================================