diff --git a/_sources/users_guide/building-a-case.txt b/_sources/users_guide/building-a-case.txt index e302fd96157..005390453b6 100644 --- a/_sources/users_guide/building-a-case.txt +++ b/_sources/users_guide/building-a-case.txt @@ -4,7 +4,7 @@ Building a Case ****************** -The following summarizes details of building the model executable. +The following describes the process of building the model executable. .. _building-the-model: @@ -17,14 +17,12 @@ After calling **case.setup**, run **case.build** to build the model executable. 1. Create the component namelists in ``$RUNDIR`` and ``$CASEROOT/CaseDocs``. 2. Create the necessary compiled libraries ``mct``, ``pio``, ``gptl`` and ``csm_share``. The libraries will be placed in a path below ``$SHAREDLIBROOT``. -3. Create the necessary component compiled libraries. - These will be placed in ``$EXEROOT/bld/lib``. -4. Create the model executable (``$MODEL.exe``), which will be placed in ``$EXEROOT``. +3. Create the necessary compiled libraries. These are be placed in ``$EXEROOT/bld/lib``. +4. Create the model executable (``$MODEL.exe``), which is placed in ``$EXEROOT``. You do not need to change the default build settings to create the executable, but it is useful to become familiar with them in order to make optimal use of the system. The CIME scripts provide you with a great deal of flexibility in customizing the build process. -The **env_build.xml** variables control various aspects of building the model executable. -Most of the variables should not be modified, but users can modify these: +The **env_build.xml** variables control various aspects of building the executable. Most of the variables should not be modified, but users can modify these: - ``$BUILD_THREADED`` @@ -32,10 +30,10 @@ Most of the variables should not be modified, but users can modify these: - ``$GMAKE_J`` -The best way to determine what xml variables are in your ``$CASEROOT`` directory is to use the ``xmlquery`` command. For usage information, run: +The best way to see what xml variables are in your ``$CASEROOT`` directory is to use the **xmlquery** command. For usage information, run: :: - ./xmlquery --help + > ./xmlquery --help To build the model, change to your ``$CASEROOT`` directory and execute **case.build**. :: @@ -43,25 +41,23 @@ To build the model, change to your ``$CASEROOT`` directory and execute **case.bu > cd $CASEROOT > ./case.build -Diagnostic comments will appear as the build proceeds. +Diagnostic comments appear as the build proceeds. -The **case.build** command generates the utility and component libraries and the model executable, and it generates build logs for each component. Each build log file is date stamped, and a pointer to the build log file for that library or component is shown. - -The build log files have names in this form: **$component.bldlog.$datestamp**. They are located in ``$BLDDIR``. If they are compressed (as indicated by a .gz file extension), then the build ran successfully. +The **case.build** command generates the utility and component libraries and the model executable, and it generates build logs for each component. Each log file is named form: **$component.bldlog.$datestamp**. They are located in ``$BLDDIR``. If they are compressed (as indicated by a .gz file extension), the build ran successfully. Invoking **case.build** creates the following directory structure in ``$EXEROOT`` if the Intel compiler is used: :: atm/, cpl/, esp/, glc/, ice/, intel/, lib/, lnd/, ocn/, rof/, wav/ -Except for **intel/** and **lib/**, each of those directories contains an **obj/** directory for the compiled object files for the target model component. +Except for **intel/** and **lib/**, each directory contains an **obj/** subdirectory for the target model component's compiled object files. -The ``mct``, ``pio``, ``gptl`` and ``csm_share`` libraries are placed in a directory tree that reflects their dependencies. See the **bldlog** for a given component to locate the library. +The *mct*, *pio*, *gptl* and *csm_share* libraries are placed in a directory tree that reflects their dependencies. See the **bldlog** for a given component to locate the library. -Special **include** modules are also placed in **lib/include**. The model executable (for example, **cesm.exe** or **acme.exe**) is placed directly in ``$EXEROOT``. +Special **include** modules are placed in **lib/include**. The model executable (**cesm.exe** or **acme.exe**, for example) is placed directly in ``$EXEROOT``. -Component namelists, component logs, output datasets, and restart files are placed in ``$RUNDIR``. -It is important to note that ``$RUNDIR`` and ``$EXEROOT`` are independent variables that are set as ``$CASEROOT/env_run.xml``. +Component namelists, component logs, output data sets, and restart files are placed in ``$RUNDIR``. +It is important to note that ``$RUNDIR`` and ``$EXEROOT`` are independent variables that are set in the **$CASEROOT/env_run.xml** file. .. _rebuilding-the-model: @@ -71,7 +67,7 @@ Rebuilding the model Rebuild the model under the following circumstances: -If either **env_build.xml** or **Macros.make** has been modified, and/or if code is added to ``SourceMods/src.*``, then it's safest to clean the build and rebuild from scratch as shown here: +If either **env_build.xml** or **Macros.make** has been modified, and/or if code is added to **SourceMods/src.**, it's safest to clean the build and rebuild from scratch as shown here: :: > cd $CASEROOT @@ -83,29 +79,41 @@ If you have ONLY modified the PE layout in **env_mach_pes.xml**, a clean may not > cd $CASEROOT > ./case.build -If the threading has been turned on or off in any component relative to the previous build, the build script should fail with the following error and suggestion that the model be rebuilt from scratch: +If the threading has been changed (turned on or off) in any component since the previous build, the build script should fail with the following error and suggestion that the model be rebuilt from scratch: :: ERROR SMP STATUS HAS CHANGED SMP_BUILD = a0l0i0o0g0c0 SMP_VALUE = a1l0i0o0g0c0 - A manual clean of your obj directories is strongly recommended + A manual clean of your obj directories is strongly recommended. You should execute the following: ./case.build --clean ./case.build ---- OR ---- - You can override this error message at your own risk by executing + You can override this error message at your own risk by executing: ./xmlchange SMP_BUILD=0 - Then rerun the build script interactively + Then rerun the build script interactively. If there is any doubt, rebuild. -The **case.build --clean** command will clean all of the model components but not support libraries such as ``mct`` and ``gptl``. -Use **case.build --clean-all** to clean everything associated with the build. +Run this to clean all of the model components (except for support libraries such as *mct* and *gptl*): + :: + + > case.build --clean + +Run this to clean everything associated with the build: + :: + + > case.build --clean-all -You can also clean an individual component using **case.build --clean compname**, where "compname" is the name of the component you want to clean (for example, atm, clm, pio and so on). Run **case.build --help** for details. +You can also clean an individual component as shown here, where "compname" is the name of the component you want to clean (for example, atm, clm, pio and so on). + :: + + > case.build --clean compname + +Review the **help** text for more information. .. _inputdata: @@ -115,19 +123,22 @@ Input data All active components and data components use input data sets. In order to run CIME and the CIME-compliant active components, a local disk needs the directory tree that is specified by the xml variable ``$DIN_LOC_ROOT`` to be populated with input data. -Input data is provided as part of the CIME release via data from a subversion input data server. It is downloaded from the server on an as-needed basis determined by the case. Data may already exist in the default local file system's input data area as specified by ``$DIN_LOC_ROOT``. (See below.) +Input data is provided as part of the CIME release via data from a subversion input data server. It is downloaded from the server on an as-needed basis determined by the case. Data may already exist in the default local file system's input data area as specified by ``$DIN_LOC_ROOT``. Input data can occupy significant space on a system, so users should share a common ``$DIN_LOC_ROOT`` directory on each system if possible. The build process handles input data as follows: -- The ``buildnml`` scripts in the various component ``cime_config`` directories create listings of required component input data sets in the ``Buildconf/$component.input_data_list`` files. +- The **buildnml** scripts in the various component **cime_config** directories create listings of required component input data sets in the **Buildconf/$component.input_data_list** files. - **check_input_data**, which is called by **case.build**, checks for the presence of the required input data files in the root directory ``$DIN_LOC_ROOT``. - If all required data sets are found on the local disk, the build can proceed. -- If any of the required input data sets are not found locally, the files that are missing will be listed. At this point, you must obtain the required data from the input data server using **check_input_data** with the **-export** option. +- If any of the required input data sets are not found locally, the files that are missing are listed. At this point, you must obtain the required data from the input data server with **check_input_data** as shown here: + :: + + check_input_data --export The **env_run.xml** variables ``$DIN_LOC_ROOT`` and ``$DIN_LOC_ROOT_CLMFORC`` determine where you should expect input data to reside on a local disk. diff --git a/_sources/users_guide/case-basics.txt b/_sources/users_guide/case-basics.txt index befb0a11e8d..0f831a446c1 100644 --- a/_sources/users_guide/case-basics.txt +++ b/_sources/users_guide/case-basics.txt @@ -8,13 +8,13 @@ Two concepts to understand before working with CIME are component sets and model - *Component sets*, which are usually referred to as "compsets," define both individual model components and any component-specific namelist or configuration settings that are used in a case. -- *Model grids* specify the grid or resolution for each component making up the model. +- *Model grids* specify the grid or resolution for each component of the model. Creating a CIME experiment or *case* requires, at a minimum, specifying a compset and a model grid. -Out-of-the-box compsets and models grids are associated with two names: a longname and an alias name. Examples of both follow. +Out-of-the-box compsets and models grids each have two names: a *longname* and an *alias* name. Examples of both follow. -The CIME regression test system requires aliases, but aliases can also be used for convenience. Compset aliases are unique; each compset alias is associated with one and only one compset. Grid aliases, on the other hand, are overloaded; the same grid alias may result in a different grid depending on the associated compset. Always confirm that the *compset longname* and the *grid longname* are correct when using aliases to create a case. +The CIME regression test system requires aliases, but aliases can also be used for convenience. *Compset aliases* are unique; each is associated with one and only one compset. *Grid aliases*, on the other hand, are overloaded; the same grid alias may result in a different grid depending on the associated compset. Always confirm that the *compset longname* and the *grid longname* are correct when using aliases to create a case. ================ Component sets @@ -24,6 +24,8 @@ A compset longname has this form:: TIME_ATM[%phys]_LND[%phys]_ICE[%phys]_OCN[%phys]_ROF[%phys]_GLC[%phys]_WAV[%phys]_ESP[_BGC%phys] +Here are the supported values for each element of the longname:: + TIME = model time period (e.g. 1850, 2000, 20TR, RCP8...) CIME supports the following values for ATM,LND,ICE,OCN,ROF,GLC,WAV and ESP. @@ -59,15 +61,14 @@ A compset longname has this form:: The OPTIONAL %phys attributes specify sub-modes of the given system. For example, DOCN%DOM is the DOCN data ocean (rather than slab-ocean) mode. ALL the possible %phys choices for each component are listed by - calling **manage_case** with the **-list** compsets argument. + calling manage_case with the -list compsets argument. ALL data models have a %phys option that corresponds to the data model mode. -As an example, the CESM compset longname (below) refers to running a pre-industrial control with active CESM components CAM, CLM, CICE, POP2, MOSART, CISM2 and WW3 in a BDRD BGC coupling scenario.:: +As an example, this actual CESM compset longname refers to running a pre-industrial control with active CESM components CAM, CLM, CICE, POP2, MOSART, CISM2 and WW3 in a BDRD BGC coupling scenario:: 1850_CAM60_CLM50%BGC_CICE_POP2%ECO_MOSART_CISM2%NOEVOLVE_WW3_BGC%BDRD -The alias for this compset is B1850. Input to **create_newcase** can be either a compset longname or a compset alias. -It is also possible to create your own custom compset. See *How do I create my own compset?* in the FAQ. +The alias for this compset is B1850. Either a compset longname or a compset alias can be input to **create_newcase**. You can also create your own custom compset. See *How do I create my own compset?* in the FAQ. =============================== Model Grids @@ -77,6 +78,8 @@ A model grid longname has the form:: a%name_l%name_oi%name_r%name_m%mask_g%name_w%name +For reference:: + a% = atmosphere grid l% = land grid oi% = ocean/sea-ice grid (must be the same) @@ -94,18 +97,18 @@ A model grid longname has the form:: be identical to the land grid. The internal CISM grid can be different, however, and is specified by the g% value. -As an example, examine this longname:: +As an example, examine this actual grid longname:: a%ne30np4_l%ne30np4_oi%gx1v7_r%r05_m%gx1v7_g%null_w%null -It refers to a model grid with a ne30np4 spectral element 1-degree atmosphere and land grids, gx1v7 Greenland pole 1-degree ocean and sea-ice grids, a 1/2 degree river routing grid, null wave and internal cism grids, and an gx1v7 ocean mask. +It refers to a model grid with a ne30np4 spectral element, 1-degree atmosphere and land grids, gx1v7 Greenland pole, 1-degree ocean and sea-ice grids, a 1/2 degree river routing grid, null wave and internal cism grids, and an gx1v7 ocean mask. The alias for this grid is ne30_g16. CIME also permits users to introduce their own :ref:`user-defined grids `. Component grids are denoted by the following naming convention: -- "[dlat]x[dlon]" are regular lon/lat finite volume grids where dlat and dlon are the approximate grid spacing. The shorthand convention is "fnn" where nn generally is a pair of numbers indicating the resolution. An example is 1.9x2.5 or f19 for the approximately "2-degree" finite volume grid. Note that CAM uses an [nlat]x[nlon] naming convention internally for this grid. +- "[dlat]x[dlon]" are regular lon/lat finite volume grids where dlat and dlon are the approximate grid spacing. The shorthand convention is "fnn" where nn generally is a pair of numbers indicating the resolution. An example is 1.9x2.5 or f19 for the approximately "2-degree" finite-volume grid. Note that CAM uses an [nlat]x[nlon] naming convention internally for this grid. - "Tnn" are spectral lon/lat grids where nn is the spectral truncation value for the resolution. The shorthand name is identical. Example: T85. @@ -121,7 +124,7 @@ Component grids are denoted by the following naming convention: Querying CIME - calling **query_config** ============================================== -The utility **$CIMEROOT/scripts/query_config** permits you to query the out-of-the-box compsets, components, grids and machines that are available for a model. +Use the utility **$CIMEROOT/scripts/query_config** to see which out-of-the-box compsets, components, grids and machines are available for a model. Optional arguments include the following: :: @@ -131,17 +134,21 @@ Optional arguments include the following: --grids --machines -If CIME is downloaded in standalone mode, only standalone CIME compsets can be queried. If CIME is part of a larger checkout that includes the prognostic components of a model, **query_config** will allow you to query all prognostic component compsets, as well. +If CIME is downloaded in standalone mode, only standalone CIME compsets can be queried. If CIME is part of a larger checkout that includes the prognostic components of a model, **query_config** will allow you to query all prognostic component compsets. -Run **query_config -- --help** to see lists of available compsets, components, grids and machines. +To see lists of available compsets, components, grids and machines, look at the **help** text: + :: + + > query_config --help **Usage examples** - To run **query_config** for compset information, use the **---compsets** option and the component name, which is **drv** in this example: + +To run **query_config** for compset information, follow this example, where **drv** is the component name: :: - query_config --compsets drv + > query_config --compsets drv - The output will be similar to this: +The output will be similar to this: :: -------------------------------------- @@ -158,12 +165,12 @@ Run **query_config -- --help** to see lists of available compsets, components, g Each model component specifies its own definitions of what can appear after the ``%`` modifier in the compset longname (for example, ``DOM`` in ``DOCN%DOM``). - To see what supported modifiers are for ``DOCN``, run **query_config** as in this example: +To see what supported modifiers are for ``DOCN``, run **query_config** as in this example: :: - query_config --component docn + > query_config --component docn - The output will be similar to this: +The output will be similar to this: :: ========================================= diff --git a/_sources/users_guide/cloning-a-case.txt b/_sources/users_guide/cloning-a-case.txt index 9105dcd3a52..ffaf3c447d5 100644 --- a/_sources/users_guide/cloning-a-case.txt +++ b/_sources/users_guide/cloning-a-case.txt @@ -6,11 +6,11 @@ Cloning a Case If you have access to a run that you want to clone, the **create_clone** command will create a new case while preserving local modifications to the case. -Here is the simplest example of using **create_clone**: +Here is a simple example: :: - cd $CIMEROOT/scripts - create_clone --case $CASEROOT --clone $CLONEROOT + > cd $CIMEROOT/scripts + > create_clone --case $CASEROOT --clone $CLONEROOT The **create_clone** script preserves any local namelist modifications made in the **user_nl_xxxx** files as well as any source code modifications in the **SourceMods** tree. Otherwise, **$CASEROOT/** directory will appear as if **create_newcase** had just been run. @@ -19,6 +19,6 @@ The **create_clone** script preserves any local namelist modifications made in t See the **help** text for more usage information. :: - create_clone --help + > create_clone --help Another approach to duplicating a case is to use the information in the case's **README.case** and **CaseStatus** files to create a new case and duplicate the relevant **xlmchange** commands that were issued in the original case. This alternative will *not* preserve any local modifications that were made to the original case, such as source-code or build-script revisions; you will need to import those changes manually. diff --git a/_sources/users_guide/create-a-case.txt b/_sources/users_guide/create-a-case.txt index ba297b0071a..7cca2cb450f 100644 --- a/_sources/users_guide/create-a-case.txt +++ b/_sources/users_guide/create-a-case.txt @@ -12,12 +12,17 @@ The first step in creating a CIME-based experiment is to use **create_newcase**. If you are not on an out-of-the box CIME-supported platform, you will need to :ref:`port ` CIME to your system before proceeding. -Review the input options for **create_newcase** by using the **---help** option. The only required arguments to **create_newcase** are: -:: +Review the input options for **create_newcase** in the **help** text. + :: - create_newcase --case [CASE] --compset [COMPSET] --res [GRID] + > create_newcase --help -CIME supports out of the box *component sets*, *model grids** and *hardware platforms*. Compsets and grids were discussed in the :ref:`previous section `. +The only required arguments to **create_newcase** are shown here: + :: + + > create_newcase --case [CASE] --compset [COMPSET] --res [GRID] + +CIME supports out-of-the-box *component sets*, *model grids* and *hardware platforms*. Compsets and grids were discussed in the :ref:`previous section `. --------------------------------- Result of calling create_newcase @@ -26,19 +31,19 @@ Result of calling create_newcase Following is a simple example of using **create_newcase** with aliases for both compset and grid names. The complete example appears in the :ref:`basic example `. -In what follows, ``$CIMEROOT`` is the full pathname of the root directory of the CIME distribution. -:: +Here, ``$CIMEROOT`` is the full pathname of the root directory of the CIME distribution. + :: > cd $CIMEROOT/scripts > create_newcase --case ~/cime/example1 --compset A --res f09_g16_rx1 -In the example, the command creates a ``$CASEROOT`` directory **~/cime/example1**. (If that directory already exists, a warning is printed and the command aborts. +In the example, the command creates a ``$CASEROOT`` directory: **~/cime/example1**. If that directory already exists, a warning is printed and the command aborts. Additional details: -- ``$CASE`` is ``example1`` (``$CASE`` can include letters, numbers, ".", and "_") +- ``$CASE`` can include letters, numbers, ".", and "_". In the example, it is ``example1``. - The compset is ``2000_DATM%NYF_SLND_DICE%SSMI_DOCN%DOM_DROF%NYF_SGLC_SWAV``. -- The model resolution is ``a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%null_w%null`` +- The model resolution is ``a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%null_w%null``. - **create_newcase** installs files in ``$CASEROOT`` to build and run the model and to optionally archive the case on the target platform. @@ -47,19 +52,17 @@ Running **create_newcase** creates various scripts, files and directories ``$CAS - ``user scripts`` ================= ===================================================================================================== - case.setup Script used to set up the case (create the case.run script, the Macros file and user_nl_xxx files) - case.build Script to build component and utility libraries and model executable - case.submit Script to submit the case to run using the machine's batch queueing system - case.st_archive Script to perform short-term archiving of output data - case.lt_archive Script to perform long-term archiving of output data - xmlchange Script to modify values in the xml files - xmlquery Script to query values in the xml files - preview_namelists Script for users to see their component namelists in ``$CASEROOT/CaseDocs`` before running the model - - .. warning:: the namelists generated in ``$CASEROOT/CaseDocs`` should not be edited by the user - - they are only there to document model behavior. - check_input_data Script for checking for various input datasets and moves them into place. + case.setup Script used to set up the case (create the case.run script, the Macros file and user_nl_xxx files). + case.build Script to build component and utility libraries and model executable. + case.submit Script to submit the case to run using the machine's batch queueing system. + case.st_archive Script to perform short-term archiving of output data. + case.lt_archive Script to perform long-term archiving of output data. + xmlchange Script to modify values in the xml files. + xmlquery Script to query values in the xml files. + preview_namelists Script for users to see their component namelists in ``$CASEROOT/CaseDocs`` before running the model. + + .. warning:: Users should not edit namelists that are generated in ``$CASEROOT/CaseDocs``. They are there only to document model behavior. + check_input_data Script for checking for various input data sets and moving them into place. pelayout Script to query and modify the NTASKS, ROOTPE, and NTHRDS for each component model. This a convenience script that can be used in place of xmlchange and xmlquery. ================= ===================================================================================================== @@ -84,17 +87,17 @@ Running **create_newcase** creates various scripts, files and directories ``$CAS env_mach_pes.xml Sets component machine-specific processor layout (see :ref:`changing pe layout` ). The settings in this are critical to a well-load-balanced simulation (see :ref:`load balancing `). - env_run.xml Sets run-time settings such as length of run, frequency of restarts, output of coupler diagnostics, - + env_run.xml Sets runtime settings such as length of run, frequency of restarts, output of coupler diagnostics, and short-term and long-term archiving. This file can be edited at any time before a job starts. - env_batch.xml Sets batch system specific settings such as wallclock time and queue name. + + env_batch.xml Sets batch system settings such as wallclock time and queue name. ===================== =============================================================================================================================== - ``User Source Mods Directory`` ===================== =============================================================================================================================== - SourceMods Top-level directory containing sub-directories for each compset component where + SourceMods Top-level directory containing subdirectories for each compset component where you can place modified source code for that component. ===================== =============================================================================================================================== @@ -108,25 +111,24 @@ Running **create_newcase** creates various scripts, files and directories ``$CAS - ``non-modifiable work directories`` ===================== =============================================================================================================================== - Buildconf/ Work directory containing scripts to generate component namelists and component and utility libraries (e.g., PIO, MCT) - - You should never have to edit the contents of this directory. + Buildconf/ Work directory containing scripts to generate component namelists and component and utility libraries + (PIO or MCT, for example). You should never have to edit the contents of this directory. LockedFiles/ Work directory that holds copies of files that should not be changed. Certain xml files are *locked* after their variables have been used by should no longer be changed. - CIME does this by *locking* a file and not permitting you to modify that file unless, depending on the file, **case.setup ---clean** or **case.build ---clean** are called. + CIME does this by *locking* a file and not permitting you to modify that file unless, depending on the file, ``case.setup --clean`` or ``case.build --clean`` is called. Tools/ Work directory containing support utility scripts. You should never need to edit the contents of this directory. ===================== =============================================================================================================================== -The ``$CASEROOT`` xml files are organized so that variables can be locked at certain points to prevent users from changing variables after they have been resolved (used) in other parts of the scripts system. +The ``$CASEROOT`` xml files are organized so that variables can be locked at certain points to prevent users from changing them after they have been resolved (used) in other parts of the scripts system. CIME does the following: - Locks variables in **env_case.xml** after **create_newcase**. -- Locks variables in **env_mach_pes.xml** are locked after **case.setup**. +- Locks variables in **env_mach_pes.xml** after **case.setup**. - Locks variables in **env_build.xml** after completion of **case.build**. @@ -134,10 +136,10 @@ Variables in **env_run.xml**, **env_batch.xml** and **env_archive.xml** are neve The **env_case.html** file can never be unlocked. -These files can be "unlocked" as follows: +These other files can be "unlocked" as follows: -- **case.setup --clean** unlocks **env_mach_pes.xml** +- To unlock **env_mach_pes.xml**, run ``case.setup --clean``. -- **case.build --clean** unlocks **env_build.xml** +- To unlock **env_build.xml**, run ``case.build --clean``. diff --git a/_sources/users_guide/introduction-and-overview.txt b/_sources/users_guide/introduction-and-overview.txt index 80a5e843f86..32de7a4ee31 100644 --- a/_sources/users_guide/introduction-and-overview.txt +++ b/_sources/users_guide/introduction-and-overview.txt @@ -5,26 +5,29 @@ Introduction ************************** -The Common Infrastructure for Modeling the Earth (CIME) provides a UNIX command-line-based user interface for +The Common Infrastructure for Modeling the Earth (CIME) provides a UNIX command-line-based interface for configuring, compiling and executing Earth system models. Part 1 of this guide explains the basic commands -needed to get a model running. +that are needed to get a model running. Prerequisites ============= -Familiarity with the basic climate modeling concepts. +Part 1 of this guide assumes that CIME and the necessary input files have been installed on +the computer you are using. If that is not the case, see Installing CIME. + +Other prerequisites: -Familiarity with UNIX command line terminals and the UNIX development environment. +- Familiarity with basic climate modeling concepts. -CIME's commands are Python scripts and require a correct version of the Python interpreter to be installed. +- Familiarity with UNIX command line terminals and the UNIX development environment. -The Python version must be greater than 2.7 but less than 3.0. Determine which version you have by typing: +- A correct version of the Python interpreter. + +CIME's commands are Python scripts and require a correct version of the Python interpreter to be installed. The Python version must be greater than 2.7 but less than 3.0. Determine which version you have by typing: :: > python --version -**NOTE:** Part 1 of this guide assumes that CIME and the necessary input files have been installed on -the computer you are using. If that is not the case, see Installing CIME. Terms and concepts @@ -32,22 +35,22 @@ Terms and concepts The following terms and concepts are ingrained in CIME and are used frequently in this documentation. -**active** vs **data** vs **stub** models: - Components of a model that solve a complex set of equations to describe the model's behavior are called +**active, data and stub models** + *active models*: Components of a model that solve a complex set of equations to describe the model's behavior are called *active* models. Sometimes they are called *prognostic* or *full* models. - CIME recognizes 7 different active models of a climate model. They are: + CIME recognizes 7 different active models. They are: atmosphere, ocean, sea-ice, land surface, river, glacier, wave An external system processing (ESP) stub-only component is also allowed. - For some climate problems, it is necessary to reduce feedbacks within the system by replacing an active model with a + *data models*: For some climate problems, it is necessary to reduce feedbacks within the system by replacing an active model with a version that sends and receives the same variables to and from other models, but with the values read from files rather than computed from the equations. The values received are ignored. These active-model substitutes are called *data models*. CIME provides data models for each of the supported components. - For some configurations, no data model is needed, so CIME provides *stub* versions that simply occupy the + *stub models*: For some configurations, no data model is needed, so CIME provides *stub* versions that simply occupy the required place in the climate execution sequence and do not send or receive any data. **case**: @@ -81,7 +84,7 @@ Before using any CIME commands, set the ``CIME_MODEL`` environment variable. In **** with the appropriate text, such as "acme" or "cesm." :: - setenv CIME_MODEL + > setenv CIME_MODEL Directory content @@ -138,7 +141,7 @@ directory structure. Discovering available cases ============================== -To identify which compsets, grids and machines your CIME-enabled model supports, use the **query_config** command found in **cime/scripts**. Use the **---help** option for more information. +To identify which compsets, grids and machines your CIME-enabled model supports, use the **query_config** command found in **cime/scripts**. See the **help** text for more information. :: @@ -147,7 +150,7 @@ To identify which compsets, grids and machines your CIME-enabled model supports, Quick start ================== -To quickly see how a case is created, configured, built and run with CIME, execute the following commands for an example. (This assumes that CIME has been ported to your current machine). +To see an example of how a case is created, configured, built and run with CIME, execute the following commands for an example. (This assumes that CIME has been ported to your current machine). :: > cd cime/scripts @@ -159,10 +162,10 @@ To quickly see how a case is created, configured, built and run with CIME, execu The output from each command is explained in the following sections. -You can follow the progress of your run by monitoring the **CaseStatus** file. +After you submit the case, you can follow the progress of your run by monitoring the **CaseStatus** file. :: > tail CaseStatus -Repeat the command until you see the message "case.run success" +Repeat the command until you see the message ``case.run success``. diff --git a/_sources/users_guide/running-a-case.txt b/_sources/users_guide/running-a-case.txt index 41eca525311..ba3caaa85e6 100644 --- a/_sources/users_guide/running-a-case.txt +++ b/_sources/users_guide/running-a-case.txt @@ -12,18 +12,17 @@ Calling **case.submit** Before you submit the case using **case.submit**, make sure the batch queue variables are set correctly for your run -targeted. The batch submissions variables are contained in the file -**$CASEROOT/env_batch.xml** under the XML ```` -and ```` elements. Make sure that you -have appropriate account numbers (``PROJECT``), time limits -(``JOB_WALLCLOCK_TIME``), and queue (``JOB_QUEUE``) for those groups.. - -Also modify **$CASEROOT/env_run.xml** for your -case using :ref:`xmlchange`. - -Once you have run **case.setup** and **case.build**, run -**case.submit** to submit the run to your machine's batch queue -system. +Those variables are contained in the file **$CASEROOT/env_batch.xml** +under the XML ```` and ```` +elements. + +Make sure that you have appropriate account numbers (``PROJECT``), time limits +(``JOB_WALLCLOCK_TIME``), and queue (``JOB_QUEUE``) for those groups. + +Also modify **$CASEROOT/env_run.xml** for your case using :ref:`xmlchange`. + +Once you have executed **case.setup** and **case.build**, run **case.submit** +to submit the run to your machine's batch queue system. :: > cd $CASEROOT @@ -39,12 +38,12 @@ When called, the **case.submit** script will: - Confirm that locked files are consistent with the current xml files. -- Run **preview_namelist**, which in turn will run each component's **buildnml** +- Run **preview_namelist**, which in turn will run each component's **buildnml**. -- Run :ref:`**check_input_data**` to verify that the required - data is present. +- Run :ref:`check_input_data` to verify that the required + data are present. -- Submit the job to the batch queue. which in turn will run the script **case.run**. +- Submit the job to the batch queue. which in turn will run the **case.run** script. Upon successful completion of the run, **case.run** will: @@ -56,19 +55,19 @@ Upon successful completion of the run, **case.run** will: - Submit the short-term archiver script **case.st_archive** to the batch queue if ``$DOUT_S`` is TRUE. -- Resubmit **case.run** if ``$RESUBMIT`` >0. +- Resubmit **case.run** if ``$RESUBMIT`` > 0. Short-term archiving will copy and move component history, log, diagnostic, and restart files from ``$RUNDIR`` to the short-term -archive directory, ``$DOUT_S_ROOT``. +archive directory ``$DOUT_S_ROOT``. --------------------------------- Monitoring case job statuses --------------------------------- The **$CASEROOT/CaseStatus** file contains a log of all the job states -and **xmlchange** commands in chronological order. An example of status -messages includes: +and **xmlchange** commands in chronological order. Here is an example of status +messages: :: 2017-02-14 15:29:50: case.setup starting @@ -92,8 +91,6 @@ messages includes: 2017-02-14 16:20:58: st_archive success --------------------------------------------------- -When the short-term archiver is done, data from ``$RUNDIR`` is in -subdirectories under ``$DOUT_S_ROOT``. .. note:: After a successful first run, set the **env_run.xml** variable @@ -113,13 +110,13 @@ Troubleshooting a job that fails --------------------------------- There are several places to look for information if a job fails. -Start with the STDOUT and STDERR file(s) in **$CASEROOT**. +Start with the **STDOUT** and **STDERR** file(s) in **$CASEROOT**. If you don't find an obvious error message there, the **$RUNDIR/$model.log.$datestamp** files will probably give you a hint. -First check **cpl.log.$datestamp**, which will often tell you -when the model failed. Then check the rest of the component log +First, check **cpl.log.$datestamp**, which will often tell you +*when* the model failed. Then check the rest of the component log files. See :ref:`troubleshooting run-time problems` for more information. @@ -134,11 +131,10 @@ for your case exist on local disk in the appropriate subdirectory of ``$DIN_LOC_ROOT``. It automatically downloads missing data. The required input data sets needed for each component are found in the -**$CASEROOT/Buildconf** directory in the files ``xxx.input_data_list``, -where ``xxx`` is the component name. These files are generated by a call +**$CASEROOT/Buildconf** directory. These files are generated by a call to **preview_namlists** and are in turn created by each component's **buildnml** script. For example, for compsets consisting only of data -models (that is, ``A`` compsets), the following files are created: +models (``A`` compsets), the following files are created: :: datm.input_data_list @@ -146,19 +142,19 @@ models (that is, ``A`` compsets), the following files are created: docn.input_data_list drof.input_data_list -You can independently verify that the required data is present locally by +You can independently verify the presence of the required data by using the following commands: :: > cd $CASEROOT - > check_input_data -help - > check_input_data -inputdata $DIN_LOC_ROOT -check + > check_input_data --help + > check_input_data --inputdata $DIN_LOC_ROOT --check If data sets are missing, obtain them from the input data server: :: > cd $CASEROOT - > check_input_data -inputdata $DIN_LOC_ROOT -export + > check_input_data --inputdata $DIN_LOC_ROOT --export .. _controlling-start-stop-restart: @@ -174,9 +170,24 @@ a flag to determine if the run should be flagged as a continuation run. At a minimum, you will need to set the variables ``$STOP_OPTION`` and ``$STOP_N``. Other driver namelist settings then will have consistent and -reasonable default values. These default settings guarantee that +reasonable default values. The default settings guarantee that restart files are produced at the end of the model run. +By default, the stop time settings are: +:: + + STOP_OPTION = ndays + STOP_N = 5 + STOP_DATE = -999 + +The default settings are appropriate only for initial testing. Before +starting a longer run, update the stop times based on the case +throughput and batch queue limits. For example, if the model runs 5 +model years/day, set ``RESUBMIT=30, STOP_OPTION= nyears, and STOP_N= +5``. The model will then run in five-year increments and stop after +30 submissions. + + --------------------------------------------------- Run-type initialization --------------------------------------------------- @@ -227,8 +238,8 @@ The case initialization type is set using the ``$RUN_TYPE`` variable in ``hybrid`` A hybrid run is initialized like a startup but it uses initialization data sets from a previous case. It is similar - somewhat analogous to a branch run with relaxed restart - constraints. A hybrid run allows users to bring together + to a branch run with relaxed restart constraints. + A hybrid run allows users to bring together combinations of initial/restart files from a previous case (specified by ``$RUN_REFCASE``) at a given model output date (specified by ``$RUN_REFDATE``). Unlike a branch run, the starting @@ -254,29 +265,6 @@ a hybrid or branch run, you must specify values for ``$RUN_REFCASE`` and ``$RUN_REFDATE``. All run startup variables are discussed in `run start control variables`_. -**A brief note on restarting runs** - -When you first begin a branch, hybrid or startup run, ``CONTINUE_RUN`` -must be set to ``FALSE``. After the job has run successfully and -there are restart files, you will need to change ``CONTINUE_RUN`` to -TRUE for the remainder of your run. Setting the ``RESUBMIT`` option to -a value > 0 will cause the ``CONTINUE_RUN`` variable to be set to ``TRUE`` -automatically upon completion of the initial run. - -By default, the stop time settings are: -:: - - STOP_OPTION = ndays - STOP_N = 5 - STOP_DATE = -999 - -The default settings are appropriate only for initial testing. Before -starting a longer run, update the stop times based on the case -throughput and batch queue limits. For example, if the model runs 5 -model years/day, set ``RESUBMIT=30, STOP_OPTION= nyears, and STOP_N= -5``. The model will then run in five-year increments, and stop after -30 submissions. - .. _controlling-output-data: ========================= @@ -286,34 +274,33 @@ Controlling output data During a model run, each model component produces its own output data sets consisting of history, initial, restart, diagnostics, output log and rpointer files. Component history files and restart files are -in netCDF format. Restart files are used to either exactly restart the +in netCDF format. Restart files are used to either restart the same model or to serve as initial conditions for other model cases. The -rpointer files are text files listing the component history and -and restart files required for restart. +rpointer files are text files that list the component history and +restart files that are required for restart. -Archiving is a phase of a model run where the generated output data is +Archiving is the phase of a model run when output data are moved from ``$RUNDIR`` to a local disk area (short-term archiving). It has no impact on the production run except to clean up disk space in the ``$RUNDIR`` and help manage user quotas. -In **env_run.xml**, several variables control the behavior of +Several variables in **env_run.xml** control the behavior of short-term archiving. This is an example of how to control the data output flow with two variable settings: - :: DOUT_S = TRUE DOUT_S_ROOT = /$SCRATCH/$user/$CASE/archive -Key points to keep in mind about short-term archiving: +The first setting above is the default, so short-term archiving is enabled. The second sets where to move files at the end of a successful run. -- Short-term archiving is enabled by default (``$DOUT_S = TRUE``). +Also: - All output data is initially written to ``$RUNDIR``. -- Unless a user explicitly turns off short-term archiving, files will - be moved to ``$DOUT_S_ROOT`` at the end of a successful model run. +- Unless you explicitly turn off short-term archiving, files are + moved to ``$DOUT_S_ROOT`` at the end of a successful model run. - Users generally should turn off short-term archiving when developing new code. @@ -353,26 +340,23 @@ for a description of output data filenames. Restarting a run ====================== -Each active component (and some data components) write restart files +Active components (and some data components) write restart files at intervals that are dictated by the driver via the setting of the ``$REST_OPTION`` and ``$REST_N`` variables in **env_run.xml**. Restart files allow the model to stop and then start again with bit-for-bit exact capability; the model output is exactly the same as if the model -had not stopped). The driver coordinates the writing of restart -files as well as the time evolution of the model. All components -receive restart and stop information from the driver and write -restarts or stop as the drives specifies. +had not stopped. The driver coordinates the writing of restart +files as well as the time evolution of the model. -Keep in mind that runs initialized as branch or hybrid runs, require +Runs that are initialized as branch or hybrid runs require restart/initial files from previous model runs (as specified by the -variables ``$RUN_REFCASE`` and ``$RUN_REFDATE``). The user must pre-stage -these required files to the case ``$RUNDIR`` (normally ``$EXEROOT/run``) +variables ``$RUN_REFCASE`` and ``$RUN_REFDATE``). Pre-stage these +iles to the case ``$RUNDIR`` (normally ``$EXEROOT/run``) before the model run starts. Normally this is done by copying the contents of the relevant **$RUN_REFCASE/rest/$RUN_REFDATE.00000** directory. Whenever a component writes a restart file, it also writes a restart -pointer file in the format **rpointer.$component**. The pointer -file contains the name of that new restart file. Upon a restart, each +pointer file in the format **rpointer.$component**. Upon a restart, each component reads the pointer file to determine which file to read in order to continue the run. These are examples of pointer files created for a component set using full active model components. @@ -403,15 +387,14 @@ back up to a previous restart. If short-term archiving is enabled, find the latest **$DOUT_S_ROOT/rest/yyyy-mm-dd-ssss/** directory and copy its contents into your run directory (``$RUNDIR``). -Make sure that the new rpointer.* files overwrite older files in -in ``$RUNDIR``, or the job may not restart in the correct place. - -You can then continue the run using the new restarts. +Make sure that the new restart pointer files overwrite older files in +in ``$RUNDIR`` or the job may not restart in the correct place. You can +then continue the run using the new restarts. Occasionally, when a run has problems restarting, it is because the -rpointer.* and restart files are out of sync. The rpointer.* files -are text files that can easily be edited to match the correct dates -of the restart and history files. All the restart files should +pointer and restart files are out of sync. The pointer files +are text files that can be edited to match the correct dates +of the restart and history files. All of the restart files should have the same date. ============================ @@ -424,8 +407,7 @@ which is set to **$CASEROOT/logs** by default. If the job aborts, log files are NOT be copied out of the ``$RUNDIR`` directory. The output data flow from a successful run depends on whether or not -short-term archiving is enabled, as it is by default. (The **env_run.xml** -variable ``$DOUT_S`` is set as ``DOUT_S=TRUE``. +short-term archiving is enabled, as it is by default. ------------- No archiving diff --git a/_sources/users_guide/setting-up-a-case.txt b/_sources/users_guide/setting-up-a-case.txt index 7ee6ceae884..eb683f5d3df 100644 --- a/_sources/users_guide/setting-up-a-case.txt +++ b/_sources/users_guide/setting-up-a-case.txt @@ -8,29 +8,23 @@ Setting up a Case Calling **case.setup** =================================== -After creating a case or changing aspects of a case, such as the pe-layout, call the **case.setup** command from ``$CASEROOT`` This creates additional files and directories in ``$CASEROOT``. They are described below. - -To see the options that are available with **case.setup**, use the **---help**. option. +After creating a case or changing aspects of a case, such as the pe-layout, call the **case.setup** command from ``$CASEROOT``. This creates additional files and directories in ``$CASEROOT``. They are described below. ============================= =============================================================================================================================== - case.run Run script containing the batch directives - - The batch directives are generated using the contents of env_mach_pes.xml. - Calling **case.setup --clean** will remove this file. + case.run Run script containing the batch directives. The directives are generated using the contents + of **env_mach_pes.xml**. Running ``case.setup --clean`` will remove this file. Macros.make File containing machine-specific makefile directives for your target platform/compiler. - This file is created if it does not already exist. - The user can modify this file to change certain aspects of the build, such as compiler flags. - - Calling **case.setup --clean** will not remove the file once it has been created. - However. if you remove or rename the Macros.make file, **case.setup** will recreate it. + The user can modify the file to change certain aspects of the build, such as compiler flags. + Running ``case.setup --clean`` will not remove the file once it has been created. + However. if you remove or rename the Macros.make file, running **case.setup** recreates it. user_nl_xxx[_NNNN] files Files where all user modifications to component namelists are made. **xxx** is any one of the set of components targeted for the case. - For example, for a full active CESM compset, **xxx** would be cam, clm, rtm, and so on. + For example, for a full active CESM compset, **xxx** is cam, clm or rtm, and so on. NNNN goes from 0001 to the number of instances of that component. (See :ref:`multiple instances`) @@ -38,12 +32,13 @@ To see the options that are available with **case.setup**, use the **---help**. For a case with 1 instance of each component (default), NNNN will not appear in the user_nl file names. - A user_nl file of a given name will only be created once. + A user_nl file of a given name is created only once. - Calling **case.setup -\ -\ clean** will *not remove* any user_nl files. + Calling ``case.setup --clean`` will *not remove* any user_nl files. Changing the number of instances in the **env_mach_pes.xml** file will cause only new user_nl files to be added to ``$CASEROOT``. + CaseDocs/ Directory that contains all the component namelists for the run. This is for reference only and files in this directory SHOULD NOT BE EDITED since they will diff --git a/_sources/users_guide/troubleshooting.txt b/_sources/users_guide/troubleshooting.txt index b67a258b2c5..e109b81a01b 100644 --- a/_sources/users_guide/troubleshooting.txt +++ b/_sources/users_guide/troubleshooting.txt @@ -11,7 +11,7 @@ Generally, **create_newcase** errors are reported to the terminal and should pro If **create_newcase** fails on a relatively generic error, first check to make sure the command-line arguments match the interface's specification. See the help text to review usage. :: - create_newcase --help + > create_newcase --help Troubleshooting job submission ------------------------------- @@ -30,7 +30,7 @@ Troubleshooting runtime problems To see if a run completed successfully, check the last several lines of the **cpl.log** file for a string like ``SUCCESSFUL TERMINATION``. A successful job also usually copies the log files to the **$CASEROOT/logs** directory. -**Note**: The first things to check when a job fails: +Check these things first when a job fails: - Did the model time out? @@ -42,7 +42,7 @@ To see if a run completed successfully, check the last several lines of the **cp If any of those things happened, take appropriate corrective action (see suggestions below) and resubmit the job. -If it is not clear any of the above caused a case to fail, then there are several places to look for error messages. +If it is not clear that any of the above caused a case to fail, there are several places to look for error messages. - Check component log files in your run directory (``$RUNDIR``). This directory is set in the **env_run.xml** file. @@ -57,9 +57,8 @@ If it is not clear any of the above caused a case to fail, then there are severa - Check any automated email from the job about why a job failed. Some sites' batch schedulers send these. -- Check the archive directory. - If a case failed, the log files or data may still have been archived. - The archiver is turned on if ``DOUT_S`` is set to TRUE in **env_run.xml**. The directory to check is **$DOUT_S_ROOT/$CASE**. +- Check the archive directory: **$DOUT_S_ROOT/$CASE**. If a case failed, the log files + or data may still have been archived. **Common errors** @@ -73,7 +72,7 @@ Another error that can cause a timeout is a slow or intermittently slow node. The **cpl.log** file normally outputs the time used for every model simulation day. To review that data, grep the **cpl.log** file for the string ``tStamp`` as shown here: :: - grep tStamp cpl.log.* | more + > grep tStamp cpl.log.* | more The output looks like this: :: @@ -98,6 +97,6 @@ Sometimes when a job times out or overflows disk space, the restart files will g With the exception of the CAM and CLM history files, all the restart files have consistent sizes. Compare the restart files against the sizes of a previous restart. If they don't match, remove them and move the previous restart into place before resubmitting the job. -See `restarting a run `_. +See `Restarting a run `_. It is not uncommon for nodes to fail on HPC systems or for access to large file systems to hang. Before you file a bug report, make sure a case fails consistently in the same place. diff --git a/searchindex.js b/searchindex.js index 1053e30844e..43f02b202f3 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ 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plhist_dir:3,dlnd_cplhist_yr_align:3,dlnd_cplhist_yr_end:3,dlnd_cplhist_yr_start:3,dlnd_fld:3,dlnd_in:[3,11,34],dlnd_in_nnn:[3,34],dlnd_nml:[3,11,12],dlon:30,dmpi:48,dn10:[2,11,12],do_budget:14,docn:4,docn_fld:5,docn_in:[5,11,34],docn_in_0001:41,docn_in_0002:41,docn_in_nnn:[5,34],docn_nml:[5,11,12],docn_ocn_in_0001:41,docn_ocn_in_0002:41,docn_som_filename:5,docn_sstdata_filename:5,docn_sstdata_year_end:5,docn_sstdata_year_start:5,document:[14,15,22,25],doe:[5,9,11,15,17,23,25,33,34,43,44,45,49],doesn:[9,42],dofil:9,doi:22,dom:[17,30,31],dom_a:17,dom_drof:[30,33],dom_i:17,dom_l:17,dom_o:17,domain:[9,11],domainfil:[9,11,12],domaininfo:[9,11,12],domap:9,domareanam:9,domfilenam:9,domfilepath:9,dommasknam:9,domtvarnam:9,domxvarnam:9,domyvarnam:9,domzvarnam:9,don:[9,11,42,44,47,48],done:[2,3,5,6,7,9,13,15,17,33,42,44,48],dopenmp:48,dot:11,doubt:29,dout_l_msroot:43,dout_s:[44,47],dout_s_root:[43,44,47],down:[40,42,43,47],download:[29,30,44,48],draw:48,drive:[2,7,44,46],driven:[43,46,48],driver:[2,3,5,6,7,9,12,13,14,15],driver_cpl:[17,22,24,31],driver_fld:[2,3,5,6,7,8],drof:4,drof_cplhist_case:6,drof_cplhist_dir:6,drof_cplhist_yr_align:6,drof_cplhist_yr_end:6,drof_cplhist_yr_start:6,drof_fld:6,drof_in:[6,11,34],drof_in_nnn:34,drof_nml:[6,11,12],drop:48,drv:[17,30,31,44],drv_flds_in:[24,41],drv_in:[17,24,34,41],drv_thread:16,dstdry1:2,dstdry2:2,dstdry3:2,dstdry4:2,dstmask:11,dstwet1:2,dstwet2:2,dstwet3:2,dstwet4:2,dtest:43,dtlimit:[9,11],dtmax:9,dtmin:9,due:[5,15,17,42,43],duplic:[32,48],durat:46,dure:[9,15,16,42,43,44],duu10n:5,dwav:4,dwav_fld:8,dwav_in:[8,11],dwav_nml:[8,11,12],dxxx_mode:12,dycor:28,dynam:[15,49],each:[2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,21,23,25,29,30,31,33,34,40,41,42,43,44,45,46,47,48,49],earli:[25,43],earlier:48,earth:[22,40,42,43,49],easi:[17,44,46,48],easier:48,easiest:17,easili:[11,12,15,43,44],east:17,eccen:9,eccentr:9,eco_mosart_cism2:30,ect:46,edit:[3,4,5,6,7,8,11,28,31,33,34,35,42,44],edited:[34,45],edu:44,effect:17,effici:34,effort:14,eight:[15,42],either:[4,6,9,14,15,25,29,30,34,41,42,43,44,47,48],elaps:9,element:[11,30,31,43,44,48],elemnet:11,elev:3,elimin:25,elsewher:11,email:47,empti:48,enabl:[5,40,44,48,49],encapsul:[9,15],encount:44,end:[2,3,5,6,9,11,14,18,25,34,35,36,37,42,43,44,47,48],energi:15,ensembl:[27,41,49],ensur:[14,16,17,18,21,23,28,34,48],ensure:48,entir:[17,44,46],entri:[11,28,31,34,40,43],entry_id:31,env:[17,25,43,46,48],env_arch:33,env_batch:[33,44,47],env_build:[29,33,34],env_cas:[31,32,33],env_mach_p:[23,29,33,34,35,41,45],env_mach_specif:[33,43,45,48],env_run:[2,3,5,6,7,8,12,14,17,25,29,33,34,37,42,44,47],environ:[16,28,33,40,43,44,45,47,48],environment_vari:43,eps_aarea:17,eps_agrid:17,eps_amask:17,eps_frac:[17,34],eps_oarea:17,eps_ogrid:17,eps_omask:17,equal:[5,9,17,34],equat:40,equinox:9,eri:[43,46],err:47,errat:47,erron:4,error:[4,11,17,29,34,36,44,47,48],ers:[43,46],ers_d:43,ert:43,esg:43,esmci:49,esmf:[15,17,25,28],esmf_regridweightgen:28,esmf_wrf_timemgr:25,esp:[29,30,40],esp_modelio:24,especi:[43,47],essenti:49,establish:[12,15,21,42],estim:[41,42],etc:[12,40,42,43,48],evap:[2,3,5,7],even:[15,34,42,46],evenli:[23,25,34],event:25,everi:[14,17,25,28,31,34,42,43,47,48],everyth:29,everywher:17,evolut:[17,44],evolv:[17,18],exact:[16,43,44,46],exactli:[2,9,11,17,18,44],examin:[2,3,5,7,8,30,46],exampl:[2,4,5,9,11,12,15,17,25,28,29,30,31,32,33,34],example1:33,example_case:[35,37],example_casep:37,exce:43,except:[2,4,5,11,17,28,29,33,37,42,44,47],exchang:[2,3,4,5,6,7,8],exclud:46,exec:43,execut:[5,9,15,22,28,29,33,37,40,41,43,44,46,48,49],exercis:[42,48],exeroot:[29,44],exist:[1,5,9,28,29,33,43,44,45],expand:5,expect:[4,12,17,18,23,25,29,43,47,48],expens:42,experi:[11,30,33,34,41],experiment:[2,42],expert:[38,41],explain:40,explan:46,explanatori:46,explicit:[25,48],explicitli:[5,44,48],express:[31,43],extend:[11,23,25,48],extens:[29,48],extent:7,extern:[5,12,15,40,44,48],extra:[9,12,47],extract:[5,17,48],extrapol:11,extrem:9,f09_g16:[5,35,37],f09_g16_rx1:33,f19:[28,30],f19_f19:46,f19_g16:[28,40,43],f90:[5,9,11,17,22,25,36],fact:[3,12],factor:[2,7,17],factorfn:2,faii_evap:7,faii_lat:7,faii_lwup:7,faii_sen:7,faii_swnet:7,faii_taui:7,faii_taux:7,fail:[29,39],failur:[46,48],fairli:23,fall:11,fall_evap:3,fall_fco2_lnd:2,fall_flxdst1:3,fall_flxdst2:3,fall_flxdst3:3,fall_flxdst4:3,fall_lat:3,fall_lwup:3,fall_sen:3,fall_swnet:3,fall_taui:3,fall_taux:3,fals:[2,3,4,5,6,7,8,9,13,48],familiar:[29,40],faoo_fco2_ocn:2,faoo_fdms_ocn:2,faq:30,fashion:[18,25,34,44],fast:48,faster:42,favor:2,faxa_bcphidri:2,faxa_bcphiwet:2,faxa_bcphodri:2,faxa_dstdry1:2,faxa_dstdry2:2,faxa_dstdry3:2,faxa_dstdry4:2,faxa_dstwet1:2,faxa_dstwet2:2,faxa_dstwet3:2,faxa_dstwet4:2,faxa_lwdn:[2,5,7],faxa_ocphidri:2,faxa_ocphiwet:2,faxa_ocphodri:2,faxa_prec:5,faxa_rain:[5,7],faxa_rainc:2,faxa_rainc_18o:2,faxa_rainc_hdo:2,faxa_rainl:2,faxa_rainl_18o:2,faxa_rainl_hdo:2,faxa_snow:[5,7],faxa_snowc:2,faxa_snowc_18o:2,faxa_snowc_hdo:2,faxa_snowl:2,faxa_snowl_18o:2,faxa_snowl_hdo:2,faxa_swndf:[2,7],faxa_swndr:[2,7],faxa_swnet:2,faxa_swvdf:[2,7],faxa_swvdr:[2,7],faxx_evap:2,faxx_lat:2,faxx_lwup:2,faxx_sen:2,faxx_taui:2,faxx_taux:2,feasibl:44,featur:[11,13,16,17,23,25,44,48],feb:11,feedback:[40,47],feel:12,few:[12,15,17,42,48],fewer:9,fhello_world_mpi:36,fieldinfo:[9,11,12],figur:15,figx1:15,file:[2,3,4,5,6,7,8],file_desc_t:9,fileatm:28,filelnd:28,filenam:[2,3,5,6,7,8,9,11,12,18,24,34,40,44],fileocn:28,fileopen:9,filepath:[9,11,12],filertm:28,fill:[5,9,11,15,17,43,48],fillalgo:[9,11],fillmask:[9,11],fillread:[9,11],fillwrit:[9,11],filter:41,find:[31,39,42,44,46],fine:[16,25,47],finish:[42,46],finit:[17,28,30],fioi_melth:[5,7],fioi_meltw:[5,7],fioi_salt:[5,7],fioi_swpen:7,fioi_taui:7,fioi_taux:7,fioo_q:[5,7],first:[5,9,11,15,17,25,28,30,31,33,34,35,37,40,42,43,44,47,48],five:[11,44],fix:[4,11,15,42],flag:[2,3,4,5,6,7,8,9],flddst1:3,fldlistfil:9,fldlistmodel:9,flexibl:[22,29,34,41,42],flgl_qice:3,flop:17,flow:[22,44],flowchart:42,flux:[2,5,7,15],flux_qacc0:7,flux_qacc:7,flux_qmin:7,flux_swpf:7,flxdst2:3,flxdst3:3,flxdst4:3,fly:11,fmulti:41,fnn:30,follow:[2,3,5,6,7,8,9,11,12,15,17,21,22,25,28,29,30,31,33,34,35,36,37,38,40,41,42,43,44,46,48],foo:48,footprint:15,forc:[2,3,5,6,7,8,15,21,23,25,43,46],force_prognostic_tru:[2,3,5,6,7,8],forgotten:48,form:[5,11,13,29,30,44,46],formal:17,format:[5,11,12,18,24,28,44,46,47],former:48,forr_rofi:6,forr_rofl:6,fortran2003:48,fortran90:36,fortran:[11,12,15,16,24,25,36,39,40],fortran_unit_test:48,forward:[11,15,25,43],found:[2,3,4,5,6,7,8,9,11,12,15,22,29,31,40,42,44,47],found_gvd:9,found_lvd:9,four:[28,48],foxx_evap:5,foxx_lat:5,foxx_lwup:5,foxx_rofi:5,foxx_rofl:5,foxx_sen:5,foxx_swnet:5,foxx_taui:5,foxx_taux:5,frac:17,frac_init:17,frac_set:17,fraclist_a:17,fraclist_g:17,fraclist_i:17,fraclist_l:17,fraclist_o:17,fraction:[5,7],fractions_:17,fractions_a:17,fractions_i:17,fractions_l:17,fractions_o:17,framework:48,freez:5,frequenc:[2,5,9,15,18,19,20],frequent:[15,40],friendli:44,from:[2,3,4],front:[5,48],frustrat:36,fswpen:5,full:[5,12,28,33,40,42,44,45,46,47,48,49],fundament:[9,12,17],further:[11,25,46],futur:[17,23,25],fv1:11,g16:28,g17:30,gain:48,gather:13,gcgcs:2,gen_cesm_map:28,gen_domain:28,gen_domain_fil:28,gen_esmf_mapping_fil:28,gen_mapping_fil:28,gener:[2,3,4,5,6,7,8,9,11,12,13,14,15,17,18,21,22,24,25,28,29,30,33,34,39,41,42,43,44,45,46,47],general_grid:15,generate:46,generic:[11,12],get:[40,43,47,48],gfrac:17,ggrid:9,giss:[2,34],git:43,github:[48,49],give:[44,48],given:[4,5,9,11,16,17,23,29,30,31,34,42,43,44,45],glacier:[3,40],glade:[11,12,48],glc:[3,28,29,30,41,42,44],glc_cplhist:3,glc_elevclass:48,glc_modelio:24,glc_nec:3,global:[9,13,15,17,28,34,48],global_segmap:15,gmake:43,gmake_j:[29,43],gnu:[36,43],goal:21,goe:45,gold:46,good:[15,33,48],gpcp:2,gptl:29,gradient:17,great:29,greater:[11,17,25,34,40],greatest:[9,11],greenland:30,grep:47,grid:[3,5,9,11,12,13,14,15],gridcel:17,gridfil:[11,28],gridmap:28,gridr:9,grids_spec_file:31,gridtyp:28,group:[2,3,4,5,6,7,8,9,11,12,15,24,31,34,44],gsmap:9,gsmapr:9,gswp3:2,guarante:[42,43,44],guid:[11,26,27,31],guidanc:47,guidelin:39,gx1v6:[5,28],gx1v6_g:33,gx1v6_r:33,gx1v6_tavg_cont:5,gx1v7:30,gx1v7_g:30,gx1v7_r:30,gxgxs:2,had:[32,34,44],half:15,hand:[30,49],handl:[9,11,15,25,29],hang:47,happen:[16,17,47,48],hardwar:[15,16,22,33,34,42,43,47],hardwir:[9,25,34,42],has:29,have:[5,9,11,12,14,15,16,17,23,25,28,29,30,31,32,33,34,37,40,41,42,43,44,46,47,48],havedata:9,heart:9,heat:5,heirarch:43,heirarchi:43,hello:36,hello_mpi:36,help:[9,11,22,29,30,32,33,34,36,40,42,43,44,45,46,47,48],helper:48,here:[1,25,27,29,31,32,33,34,36,40,43,44,47,48],hhmmss:[44,47],hierarchi:12,high:[15,22,31,42],higher:[15,17,25],highest:15,highli:[9,28],hint:44,hist:44,histor:17,histori:[2,3,5,6,12],hit:47,hold:33,home:[43,46],homebrew:43,hopefulli:11,host:43,hostnam:[28,40],hour:[2,11,25,36,42,44],hourli:[9,11,15],how:[1,2,3,4,5,6,7,8,9,11,22,26,28,30,34,36,39,40,42,43,44,46,47],howev:[2,5,12,15,17,30,41,44,45,47,48],hpc:47,hpss:44,html:33,http:[43,44,48,49],hub:49,humid:2,i2x_i:17,iaf:[2,5,30,31],iaf_docn:30,iaf_drof:30,iaf_sglc_swav:30,iaf_slnd_dice:30,ice2atm:17,ice:5,ice_cov:5,ice_in:34,ice_in_0001:41,ice_in_0002:41,ice_modelio:24,ice_pres:[3,7],icefrac:5,icesst:5,ideal:[15,42],idealli:15,ident:[9,12,15,17,18,25,28,30,34,37,43],identifi:[2,9,31,34,40,42,43],idl:[15,34,42],ifrac:[2,5,7,17],ifrad:17,ignor:[9,11,40,41,44],ijhpca:[15,25],illustr:[12,41,46],imag:15,imager:7,imbal:[15,42],immedi:48,impact:[9,13,17,25,34,42,44,46],implemenent:9,implement:[2,9,11,15,16,17,18],impli:43,implicit:36,important:32,improv:[9,15,17,34,42],inabl:17,inact:34,inc_netcdf:5,inc_pnetcdf:9,incident:48,includ:[2,5,9,11,12,17,18,25,29,30,33,34,35,37,40,42,44,49],inconsist:[17,43],incorpor:44,increas:[15,35,42,47],increment:44,incur:25,inde:11,indefinit:11,indeped:25,index:[0,10,11,20,26,27,39,49],indic:[28,29,30,34,42,44,46,47],indirectli:48,individu:[15,16,17,22,29,30,42,44],industri:[30,44],industrial:43,infin:48,infinit:17,info:9,infodata:21,inform:[5,9,11,12,15,17,18,25,29,30,31,32,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a Coupled Model with CIME","1. Introduction","5. Data Atmosphere (DATM)","6. Data Land (DLND)","4. Data Model Science","8. Data Ocean (DOCN)","9. Data River (DROF)","7. Data Ice (DICE)","10. Data Wave (DWAV)","3. Design Details","CIME Data Models","2. Input Streams","1. Introduction","3.5. Bit-for-bit flag","3.7. Mass and Heat Budgets","2. Design","3.4. Driver Threading Control","3.2. Grids","3.6. History and Restarts","3. Implementation","CIME Driver/Coupler","3.3. Initialization and Restart","1. Introduction","3.8. Multi-instance Functionality","3.9. More on Driver Namelists","3.1. Time Management","Welcome to the CIME documentation!","Miscellaneous Tools","7. Adding new cases","5. Building a Case","2. The basics of CIME cases","1. CIME internals","8. Cloning a Case","3. Creating a Case","7. Customizing a Case","8.2. A Basic Example","8.1. MPI example","8.3. Setting up a branch or hybrid run","8. FAQ","CIME User’s Guide Part 1: Basic Usage","1. Introduction","6. Multi-instance component functionality","3. Optimizing Processor Layout","2. Porting and Validating CIME on a new Platform","6. Running a Case","4. Setting up a Case","4. Testing with create_test","9. Troubleshooting","5. 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d_cplhist_yr_align:3,dlnd_cplhist_yr_end:3,dlnd_cplhist_yr_start:3,dlnd_fld:3,dlnd_in:[3,11,34],dlnd_in_nnn:[3,34],dlnd_nml:[3,11,12],dlon:30,dmpi:48,dn10:[2,11,12],do_budget:14,docn:4,docn_fld:5,docn_in:[5,11,34],docn_in_0001:41,docn_in_0002:41,docn_in_nnn:[5,34],docn_nml:[5,11,12],docn_ocn_in_0001:41,docn_ocn_in_0002:41,docn_som_filename:5,docn_sstdata_filename:5,docn_sstdata_year_end:5,docn_sstdata_year_start:5,document:[14,15,22,25],doe:[5,9,11,15,17,23,25,33,34,43,44,45,49],doesn:[9,42],dofil:9,doi:22,dom:[17,30,31],dom_a:17,dom_drof:[30,33],dom_i:17,dom_l:17,dom_o:17,domain:[9,11],domainfil:[9,11,12],domaininfo:[9,11,12],domap:9,domareanam:9,domfilenam:9,domfilepath:9,dommasknam:9,domtvarnam:9,domxvarnam:9,domyvarnam:9,domzvarnam:9,don:[9,11,42,44,47,48],done:[2,3,5,6,7,9,13,15,17,33,42,44,48],dopenmp:48,dot:11,doubt:29,dout_l_msroot:43,dout_s:44,dout_s_root:[43,44,47],down:[40,42,43,47],download:[29,30,44,48],draw:48,drive:[2,7,46],driven:[43,46,48],driver:[2,3,5,6,7,9,12,13,14,15],driver_cpl:[17,22,24,31],driver_fld:[2,3,5,6,7,8],drof:4,drof_cplhist_case:6,drof_cplhist_dir:6,drof_cplhist_yr_align:6,drof_cplhist_yr_end:6,drof_cplhist_yr_start:6,drof_fld:6,drof_in:[6,11,34],drof_in_nnn:34,drof_nml:[6,11,12],drop:48,drv:[17,30,31,44],drv_flds_in:[24,41],drv_in:[17,24,34,41],drv_thread:16,dstdry1:2,dstdry2:2,dstdry3:2,dstdry4:2,dstmask:11,dstwet1:2,dstwet2:2,dstwet3:2,dstwet4:2,dtest:43,dtlimit:[9,11],dtmax:9,dtmin:9,due:[5,15,17,42,43],duplic:[32,48],durat:46,dure:[9,15,16,42,43,44],duu10n:5,dwav:4,dwav_fld:8,dwav_in:[8,11],dwav_nml:[8,11,12],dxxx_mode:12,dycor:28,dynam:[15,49],each:[2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,21,23,25,29,30,31,33,34,40,41,42,43,44,45,46,47,48,49],earli:[25,43],earlier:48,earth:[22,40,42,43,49],easi:[17,44,46,48],easier:48,easiest:17,easili:[11,12,15,43],east:17,eccen:9,eccentr:9,eco_mosart_cism2:30,ect:46,edit:[3,4,5,6,7,8,11,28,31,33,34,35,42,44],edited:[34,45],edu:44,effect:17,effici:34,effort:14,eight:[15,42],either:[4,6,9,14,15,25,29,30,34,41,42,43,44,47,48],elaps:9,element:[11,30,31,43,44,48],elemnet:11,elev:3,elimin:25,elsewher:11,email:47,empti:48,enabl:[5,40,44,48,49],encapsul:[9,15],encount:44,end:[2,3,5,6,9,11,14,18,25,34,35,36,37,42,43,44,47,48],energi:15,ensembl:[27,41,49],ensur:[14,16,17,18,21,23,28,34,48],ensure:48,entir:[17,44,46],entri:[11,28,31,34,40,43],entry_id:31,env:[17,25,43,46,48],env_arch:33,env_batch:[33,44,47],env_build:[29,33,34],env_cas:[31,32,33],env_mach_p:[23,29,33,34,35,41,45],env_mach_specif:[33,43,45,48],env_run:[2,3,5,6,7,8,12,14,17,25,29,33,34,37,42,44,47],environ:[16,28,33,40,43,44,45,47,48],environment_vari:43,eps_aarea:17,eps_agrid:17,eps_amask:17,eps_frac:[17,34],eps_oarea:17,eps_ogrid:17,eps_omask:17,equal:[5,9,17,34],equat:40,equinox:9,eri:[43,46],err:47,errat:47,erron:4,error:[4,11,17,29,34,36,44,47,48],ers:[43,46],ers_d:43,ert:43,esg:43,esmci:49,esmf:[15,17,25,28],esmf_regridweightgen:28,esmf_wrf_timemgr:25,esp:[29,30,40],esp_modelio:24,especi:[43,47],essenti:49,establish:[12,15,21,42],estim:[41,42],etc:[12,40,42,43,48],evap:[2,3,5,7],even:[15,34,42,46],evenli:[23,25,34],event:25,everi:[14,17,25,28,31,34,42,43,47,48],everyth:29,everywher:17,evolut:[17,44],evolv:[17,18],exact:[16,43,44,46],exactli:[2,9,11,17,18,44],examin:[2,3,5,7,8,30,46],exampl:[2,4,5,9,11,12,15,17,25,28,29,30,31,32,33,34],example1:33,example_case:[35,37],example_casep:37,exce:43,except:[2,4,5,11,17,28,29,33,37,42,44,47],exchang:[2,3,4,5,6,7,8],exclud:46,exec:43,execut:[5,9,15,22,28,29,33,37,40,41,43,44,46,48,49],exercis:[42,48],exeroot:[29,44],exist:[1,5,9,28,29,33,43,44,45],expand:5,expect:[4,12,17,18,23,25,29,43,47,48],expens:42,experi:[11,30,33,34,41],experiment:[2,42],expert:[38,41],explain:40,explan:46,explanatori:46,explicit:[25,48],explicitli:[5,44,48],express:[31,43],extend:[11,23,25,48],extens:[29,48],extent:7,extern:[5,12,15,40,44,48],extra:[9,12,47],extract:[5,17,48],extrapol:11,extrem:9,f09_g16:[5,35,37],f09_g16_rx1:33,f19:[28,30],f19_f19:46,f19_g16:[28,40,43],f90:[5,9,11,17,22,25,36],fact:[3,12],factor:[2,7,17],factorfn:2,faii_evap:7,faii_lat:7,faii_lwup:7,faii_sen:7,faii_swnet:7,faii_taui:7,faii_taux:7,fail:[29,39],failur:[46,48],fairli:23,fall:11,fall_evap:3,fall_fco2_lnd:2,fall_flxdst1:3,fall_flxdst2:3,fall_flxdst3:3,fall_flxdst4:3,fall_lat:3,fall_lwup:3,fall_sen:3,fall_swnet:3,fall_taui:3,fall_taux:3,fals:[2,3,4,5,6,7,8,9,13,48],familiar:[29,40],faoo_fco2_ocn:2,faoo_fdms_ocn:2,faq:30,fashion:[18,25,34,44],fast:48,faster:42,favor:2,faxa_bcphidri:2,faxa_bcphiwet:2,faxa_bcphodri:2,faxa_dstdry1:2,faxa_dstdry2:2,faxa_dstdry3:2,faxa_dstdry4:2,faxa_dstwet1:2,faxa_dstwet2:2,faxa_dstwet3:2,faxa_dstwet4:2,faxa_lwdn:[2,5,7],faxa_ocphidri:2,faxa_ocphiwet:2,faxa_ocphodri:2,faxa_prec:5,faxa_rain:[5,7],faxa_rainc:2,faxa_rainc_18o:2,faxa_rainc_hdo:2,faxa_rainl:2,faxa_rainl_18o:2,faxa_rainl_hdo:2,faxa_snow:[5,7],faxa_snowc:2,faxa_snowc_18o:2,faxa_snowc_hdo:2,faxa_snowl:2,faxa_snowl_18o:2,faxa_snowl_hdo:2,faxa_swndf:[2,7],faxa_swndr:[2,7],faxa_swnet:2,faxa_swvdf:[2,7],faxa_swvdr:[2,7],faxx_evap:2,faxx_lat:2,faxx_lwup:2,faxx_sen:2,faxx_taui:2,faxx_taux:2,feasibl:44,featur:[11,13,16,17,23,25,44,48],feb:11,feedback:[40,47],feel:12,few:[12,15,17,42,48],fewer:9,fhello_world_mpi:36,fieldinfo:[9,11,12],figur:15,figx1:15,file:[2,3,4,5,6,7,8],file_desc_t:9,fileatm:28,filelnd:28,filenam:[2,3,5,6,7,8,9,11,12,18,24,34,40,44],fileocn:28,fileopen:9,filepath:[9,11,12],filertm:28,fill:[5,9,11,15,17,43,48],fillalgo:[9,11],fillmask:[9,11],fillread:[9,11],fillwrit:[9,11],filter:41,find:[31,39,42,44,46],fine:[16,25,47],finish:[42,46],finit:[17,28,30],fioi_melth:[5,7],fioi_meltw:[5,7],fioi_salt:[5,7],fioi_swpen:7,fioi_taui:7,fioi_taux:7,fioo_q:[5,7],first:[5,9,11,15,17,25,28,30,31,33,34,35,37,40,42,43,44,47,48],five:[11,44],fix:[4,11,15,42],flag:[2,3,4,5,6,7,8,9],flddst1:3,fldlistfil:9,fldlistmodel:9,flexibl:[22,29,34,41,42],flgl_qice:3,flop:17,flow:[22,44],flowchart:42,flux:[2,5,7,15],flux_qacc0:7,flux_qacc:7,flux_qmin:7,flux_swpf:7,flxdst2:3,flxdst3:3,flxdst4:3,fly:11,fmulti:41,fnn:30,follow:[2,3,5,6,7,8,9,11,12,15,17,21,22,25,28,29,30,31,33,34,35,36,37,38,40,41,42,43,44,46,48],foo:48,footprint:15,forc:[2,3,5,6,7,8,15,21,23,25,43,46],force_prognostic_tru:[2,3,5,6,7,8],forgotten:48,form:[5,11,13,29,30,44,46],formal:17,format:[5,11,12,18,24,28,44,46,47],former:48,forr_rofi:6,forr_rofl:6,fortran2003:48,fortran90:36,fortran:[11,12,15,16,24,25,36,39,40],fortran_unit_test:48,forward:[11,15,25,43],found:[2,3,4,5,6,7,8,9,11,12,15,22,29,31,40,42,44,47],found_gvd:9,found_lvd:9,four:[28,48],foxx_evap:5,foxx_lat:5,foxx_lwup:5,foxx_rofi:5,foxx_rofl:5,foxx_sen:5,foxx_swnet:5,foxx_taui:5,foxx_taux:5,frac:17,frac_init:17,frac_set:17,fraclist_a:17,fraclist_g:17,fraclist_i:17,fraclist_l:17,fraclist_o:17,fraction:[5,7],fractions_:17,fractions_a:17,fractions_i:17,fractions_l:17,fractions_o:17,framework:48,freez:5,frequenc:[2,5,9,15,18,19,20],frequent:[15,40],friendli:44,from:[2,3,4],front:[5,48],frustrat:36,fswpen:5,full:[5,12,28,33,40,42,44,45,46,47,48,49],fundament:[9,12,17],further:[11,25,46],futur:[17,23,25],fv1:11,g16:28,g17:30,gain:48,gather:13,gcgcs:2,gen_cesm_map:28,gen_domain:28,gen_domain_fil:28,gen_esmf_mapping_fil:28,gen_mapping_fil:28,gener:[2,3,4,5,6,7,8,9,11,12,13,14,15,17,18,21,22,24,25,28,29,30,33,34,39,41,42,43,44,45,46,47],general_grid:15,generate:46,generic:[11,12],get:[40,43,47,48],gfrac:17,ggrid:9,giss:[2,34],git:43,github:[48,49],give:[44,48],given:[4,5,9,11,16,17,23,29,30,31,34,42,43,44,45],glacier:[3,40],glade:[11,12,48],glc:[3,28,29,30,41,42,44],glc_cplhist:3,glc_elevclass:48,glc_modelio:24,glc_nec:3,global:[9,13,15,17,28,34,48],global_segmap:15,gmake:43,gmake_j:[29,43],gnu:[36,43],goal:21,goe:45,gold:46,good:[15,33,48],gpcp:2,gptl:29,gradient:17,great:29,greater:[11,17,25,34,40],greatest:[9,11],greenland:30,grep:47,grid:[3,5,9,11,12,13,14,15],gridcel:17,gridfil:[11,28],gridmap:28,gridr:9,grids_spec_file:31,gridtyp:28,group:[2,3,4,5,6,7,8,9,11,12,15,24,31,34,44],gsmap:9,gsmapr:9,gswp3:2,guarante:[42,43,44],guid:[11,26,27,31],guidanc:47,guidelin:39,gx1v6:[5,28],gx1v6_g:33,gx1v6_r:33,gx1v6_tavg_cont:5,gx1v7:30,gx1v7_g:30,gx1v7_r:30,gxgxs:2,had:[32,34,44],half:15,hand:[30,49],handl:[9,11,15,25,29],hang:47,happen:[16,17,47,48],hardwar:[15,16,22,33,34,42,43,47],hardwir:[9,25,34,42],has:29,have:[5,9,11,12,14,15,16,17,23,25,28,29,30,31,32,33,34,37,40,41,42,43,44,46,47,48],havedata:9,heart:9,heat:5,heirarch:43,heirarchi:43,hello:36,hello_mpi:36,help:[9,11,22,29,30,32,33,34,36,40,42,43,44,46,47,48],helper:48,here:[1,25,27,29,30,31,32,33,34,36,40,43,44,47,48],hhmmss:[44,47],hierarchi:12,high:[15,22,31,42],higher:[15,17,25],highest:15,highli:[9,28],hint:44,hist:44,histor:17,histori:[2,3,5,6,12],hit:47,hold:33,home:[43,46],homebrew:43,hopefulli:11,host:43,hostnam:[28,40],hour:[2,11,25,36,42,44],hourli:[9,11,15],how:[1,2,3,4,5,6,7,8,9,11,22,26,28,30,34,36,39,40,42,43,44,46,47],howev:[2,5,12,15,17,30,41,44,45,47,48],hpc:47,hpss:44,html:33,http:[43,44,48,49],hub:49,humid:2,i2x_i:17,iaf:[2,5,30,31],iaf_docn:30,iaf_drof:30,iaf_sglc_swav:30,iaf_slnd_dice:30,ice2atm:17,ice:5,ice_cov:5,ice_in:34,ice_in_0001:41,ice_in_0002:41,ice_modelio:24,ice_pres:[3,7],icefrac:5,icesst:5,ideal:[15,42],idealli:15,ident:[9,12,15,17,18,25,28,30,34,37,43],identifi:[2,9,31,34,40,42,43],idl:[15,34,42],ifrac:[2,5,7,17],ifrad:17,ignor:[9,11,40,41,44],ijhpca:[15,25],illustr:[12,41,46],imag:15,imager:7,imbal:[15,42],immedi:48,impact:[9,13,17,25,34,42,44,46],implemenent:9,implement:[2,9,11,15,16,17,18],impli:43,implicit:36,important:32,improv:[9,15,17,34,42],inabl:17,inact:34,inc_netcdf:5,inc_pnetcdf:9,incident:48,includ:[2,5,9,11,12,17,18,25,29,30,33,34,35,37,40,42,44,49],inconsist:[17,43],incorpor:44,increas:[15,35,42,47],increment:44,incur:25,inde:11,indefinit:11,indeped:25,index:[0,10,11,20,26,27,39,49],indic:[28,29,30,34,42,44,46,47],indirectli:48,individu:[15,16,17,22,29,30,42,44],industri:[30,44],industrial:43,infin:48,infinit:17,info:9,infodata:21,inform:[5,9,11,12,15,17,18,25,29,30,31,32,34,40,42,43,44,46,47,48],in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a Coupled Model with CIME","1. Introduction","5. Data Atmosphere (DATM)","6. Data Land (DLND)","4. Data Model Science","8. Data Ocean (DOCN)","9. Data River (DROF)","7. Data Ice (DICE)","10. Data Wave (DWAV)","3. Design Details","CIME Data Models","2. Input Streams","1. Introduction","3.5. Bit-for-bit flag","3.7. Mass and Heat Budgets","2. Design","3.4. Driver Threading Control","3.2. Grids","3.6. History and Restarts","3. Implementation","CIME Driver/Coupler","3.3. Initialization and Restart","1. Introduction","3.8. Multi-instance Functionality","3.9. More on Driver Namelists","3.1. Time Management","Welcome to the CIME documentation!","Miscellaneous Tools","7. Adding new cases","5. Building a Case","2. The basics of CIME cases","1. CIME internals","8. Cloning a Case","3. Creating a Case","7. Customizing a Case","8.2. A Basic Example","8.1. MPI example","8.3. Setting up a branch or hybrid run","8. FAQ","CIME User’s Guide Part 1: Basic Usage","1. Introduction","6. Multi-instance component functionality","3. Optimizing Processor Layout","2. Porting and Validating CIME on a new Platform","6. Running a Case","4. Setting up a Case","4. Testing with create_test","9. Troubleshooting","5. Fortran Unit Testing","What is CIME?"],titleterms:{"case":[28,29,30,32,33,34,39,40,44,45,47],"class":48,"default":40,"function":[23,41],"long":44,"new":[28,43,48],"short":44,acme:[34,46],activ:34,add:48,adding:[28,46,48],archiv:44,archive:44,area:17,assertion:48,atmospher:[2,34],avail:40,back:44,base:48,baselin:46,basic:[30,35,39],batch:[31,43],between:[2,3,5,6,7,8],bit:13,branch:37,budget:14,build:[0,29,48],call:[29,30,33,44,45],cam:34,cesm:[5,34],check:17,cime:[0,10,20,26,30,31,39,40,43,48,49],cism:34,climat:40,clm:34,clock:25,clone:32,compil:[31,43],compon:[15,28,30,31,34,41],compset:[28,31],concept:40,concurr:15,config_batch:43,config_compil:43,config_machin:43,configur:17,content:[26,40],control:[16,44],correct:17,coupl:[0,15,25],coupler:20,creat:[5,33],create_newcas:33,create_test:46,creation:47,custom:[11,34],data:[2,3,4,5,6,7,8,9,10,11,29,34,42,44],datamod:[2,3,5,6,7,8],datm:[2,34],datm_mode:2,defin:[31,48],descript:11,design:[9,12,15],detail:[9,48],develop:49,dice:[7,34],dice_mode:7,direct:43,directori:40,discov:40,dlnd:[3,34],dlnd_mode:3,docn:[5,34],docn_mode:5,document:[26,48],domain:17,driver:[16,20,24,25,34],drof:[6,8,34],drof_mode:[6,8],dwav:8,dwav_mode:8,exampl:[35,36,48],fail:44,faq:38,field:[2,3,5,6,7,8],file:[9,11,34,43,48],find:48,flag:13,flux:17,fortran:48,fraction:17,frequenc:25,from:5,fulli:5,gener:48,grid:[17,28,30,31],guid:39,guidelin:48,heat:14,histori:18,how:48,hybrid:37,ice:7,implement:19,independ:[2,3,5,6,7,8],indice:[0,10,20,26,27,39,49],initi:44,initial:21,input:[5,11,12,29,44],instanc:[23,41],interfac:15,intern:[2,3,5,6,7,8,31,39],interpol:17,introduct:[1,12,22,40,48],job:[44,47],kei:40,land:[3,34],layout:[34,42],librari:43,limit:42,loop:25,machin:[31,43,48],manag:[25,46],manage_testlist:46,map:17,mass:14,mct:15,memori:15,method:48,miscellan:27,mode:5,model:[0,4,9,10,15,29,30,31,34,40,42,44],modifi:34,monitor:44,more:[24,48],mpi:36,multi:[23,41],name:[2,3,5,6,7,8],namelist:[2,3,5,6,7,8,11,12,24,34],next:12,ocean:[5,34],onli:5,optimiz:42,option:43,order:48,output:44,overview:[11,12,15,48,49],packag:43,parallel:15,part:39,path:43,perform:15,pfunit:48,platform:43,pop2:34,port:[39,43],prerequisit:40,previou:44,problem:47,processor:42,prognost:5,queri:30,query_config:30,quick:40,rebuild:29,regress:46,relationship:[2,3,5,6,7,8],requir:43,restart:[9,18,21,44],result:[33,44],river:[6,34],rtm:34,run:[5,37,44,48],runtim:47,scienc:4,script:46,sea:34,section:12,sequenc:15,set:[30,31,34,37,40,42,45],setup:[45,48],shr_strdata_nml:11,some:40,specif:[31,34,43],sstdata:5,standard:17,start:[40,44],status:44,step:43,stop:44,stream:[2,3,5,6,7,8,11,34],structur:9,subdirectori:40,submiss:47,submit:44,support:48,system:[31,48],tabl:[0,10,20,26,27,39,49],target:31,teardown:48,term:[40,44],test:[39,46,48],thread:16,through:9,time:[25,42],todo:46,tool:27,toolkit:15,trigrid:17,troubleshoot:[44,47],type:44,unit:48,usage:39,use:39,user:39,using:[42,46],valid:[2,3,5,6,7,43],valu:[2,3,5,6,7,8,11],variabl:[2,3,5,6,7,8],wave:8,welcom:26,what:[48,49],where:[31,49],write:48,xml:[2,3,5,6,7,8,34,43,48],your:[43,48]}}) \ No newline at end of file diff --git a/users_guide/building-a-case.html b/users_guide/building-a-case.html index 32e612284ca..d9028374b94 100644 --- a/users_guide/building-a-case.html +++ b/users_guide/building-a-case.html @@ -96,7 +96,7 @@

Quick search

5. Building a Case

-

The following summarizes details of building the model executable.

+

The following describes the process of building the model executable.

5.1. Calling case.build

After calling case.setup, run case.build to build the model executable. Running this will:

@@ -104,20 +104,18 @@

Quick search

  • Create the component namelists in $RUNDIR and $CASEROOT/CaseDocs.
  • Create the necessary compiled libraries mct, pio, gptl and csm_share. The libraries will be placed in a path below $SHAREDLIBROOT.
    • -
  • Create the necessary component compiled libraries. -These will be placed in $EXEROOT/bld/lib.
    • -
  • Create the model executable ($MODEL.exe), which will be placed in $EXEROOT.
    • +
  • Create the necessary compiled libraries. These are be placed in $EXEROOT/bld/lib.
    • +
  • Create the model executable ($MODEL.exe), which is placed in $EXEROOT.

    • You do not need to change the default build settings to create the executable, but it is useful to become familiar with them in order to make optimal use of the system. The CIME scripts provide you with a great deal of flexibility in customizing the build process.

    -

    The env_build.xml variables control various aspects of building the model executable. -Most of the variables should not be modified, but users can modify these:

    +

    The env_build.xml variables control various aspects of building the executable. Most of the variables should not be modified, but users can modify these:

    • $BUILD_THREADED
    • $DEBUG
    • $GMAKE_J
    -

    The best way to determine what xml variables are in your $CASEROOT directory is to use the xmlquery command. For usage information, run:

    -
    ./xmlquery --help
+
    The best way to see what xml variables are in your $CASEROOT directory is to use the xmlquery command. For usage information, run:
    
+
    > ./xmlquery --help
 
    
 
    
 
    To build the model, change to your $CASEROOT directory and execute case.build.
    
@@ -125,23 +123,22 @@ 
    Quick search
    
 > ./case.build
    -

    Diagnostic comments will appear as the build proceeds.

    -

    The case.build command generates the utility and component libraries and the model executable, and it generates build logs for each component. Each build log file is date stamped, and a pointer to the build log file for that library or component is shown.

    -

    The build log files have names in this form: $component.bldlog.$datestamp. They are located in $BLDDIR. If they are compressed (as indicated by a .gz file extension), then the build ran successfully.

    +

    Diagnostic comments appear as the build proceeds.

    +

    The case.build command generates the utility and component libraries and the model executable, and it generates build logs for each component. Each log file is named form: $component.bldlog.$datestamp. They are located in $BLDDIR. If they are compressed (as indicated by a .gz file extension), the build ran successfully.

    Invoking case.build creates the following directory structure in $EXEROOT if the Intel compiler is used:

    atm/, cpl/, esp/, glc/, ice/, intel/, lib/, lnd/, ocn/, rof/, wav/
    -

    Except for intel/ and lib/, each of those directories contains an obj/ directory for the compiled object files for the target model component.

    -

    The mct, pio, gptl and csm_share libraries are placed in a directory tree that reflects their dependencies. See the bldlog for a given component to locate the library.

    -

    Special include modules are also placed in lib/include. The model executable (for example, cesm.exe or acme.exe) is placed directly in $EXEROOT.

    -

    Component namelists, component logs, output datasets, and restart files are placed in $RUNDIR. -It is important to note that $RUNDIR and $EXEROOT are independent variables that are set as $CASEROOT/env_run.xml.

    +

    Except for intel/ and lib/, each directory contains an obj/ subdirectory for the target model component’s compiled object files.

    +

    The mct, pio, gptl and csm_share libraries are placed in a directory tree that reflects their dependencies. See the bldlog for a given component to locate the library.

    +

    Special include modules are placed in lib/include. The model executable (cesm.exe or acme.exe, for example) is placed directly in $EXEROOT.

    +

    Component namelists, component logs, output data sets, and restart files are placed in $RUNDIR. +It is important to note that $RUNDIR and $EXEROOT are independent variables that are set in the $CASEROOT/env_run.xml file.

    5.2. Rebuilding the model

    Rebuild the model under the following circumstances:

    -

    If either env_build.xml or Macros.make has been modified, and/or if code is added to SourceMods/src.*, then it’s safest to clean the build and rebuild from scratch as shown here:

    +

    If either env_build.xml or Macros.make has been modified, and/or if code is added to SourceMods/src., it’s safest to clean the build and rebuild from scratch as shown here:

    > cd $CASEROOT
 > ./case.build --clean
    @@ -151,38 +148,60 @@

    Quick search

    > ./case.build
    -

    If the threading has been turned on or off in any component relative to the previous build, the build script should fail with the following error and suggestion that the model be rebuilt from scratch:

    +

    If the threading has been changed (turned on or off) in any component since the previous build, the build script should fail with the following error and suggestion that the model be rebuilt from scratch:

    ERROR SMP STATUS HAS CHANGED
 SMP_BUILD = a0l0i0o0g0c0
 SMP_VALUE = a1l0i0o0g0c0
-A manual clean of your obj directories is strongly recommended
+A manual clean of your obj directories is strongly recommended.
 You should execute the following:
    ./case.build --clean
    ./case.build
 
  ---- OR ----
 
- You can override this error message at your own risk by executing
+ You can override this error message at your own risk by executing:
    ./xmlchange SMP_BUILD=0
- Then rerun the build script interactively
+ Then rerun the build script interactively.

    If there is any doubt, rebuild.

    -

    The case.build –clean command will clean all of the model components but not support libraries such as mct and gptl. -Use case.build –clean-all to clean everything associated with the build.

    -

    You can also clean an individual component using case.build –clean compname, where “compname” is the name of the component you want to clean (for example, atm, clm, pio and so on). Run case.build –help for details.

    +
    +
    Run this to clean all of the model components (except for support libraries such as mct and gptl):
    +
    > case.build --clean
+
    +
    +
    +
    Run this to clean everything associated with the build:
    +
    > case.build --clean-all
+
    +
    +
    +
    You can also clean an individual component as shown here, where “compname” is the name of the component you want to clean (for example, atm, clm, pio and so on).
    +
    > case.build --clean compname
+
    +
    +
    +
    +

    Review the help text for more information.

    5.3. Input data

    All active components and data components use input data sets. In order to run CIME and the CIME-compliant active components, a local disk needs the directory tree that is specified by the xml variable $DIN_LOC_ROOT to be populated with input data.

    -

    Input data is provided as part of the CIME release via data from a subversion input data server. It is downloaded from the server on an as-needed basis determined by the case. Data may already exist in the default local file system’s input data area as specified by $DIN_LOC_ROOT. (See below.)

    +

    Input data is provided as part of the CIME release via data from a subversion input data server. It is downloaded from the server on an as-needed basis determined by the case. Data may already exist in the default local file system’s input data area as specified by $DIN_LOC_ROOT.

    Input data can occupy significant space on a system, so users should share a common $DIN_LOC_ROOT directory on each system if possible.

    The build process handles input data as follows:

    -
      -
    • The buildnml scripts in the various component cime_config directories create listings of required component input data sets in the Buildconf/$component.input_data_list files.
      • -
    • check_input_data, which is called by case.build, checks for the presence of the required input data files in the root directory $DIN_LOC_ROOT.
      • -
    • If all required data sets are found on the local disk, the build can proceed.
      • -
    • If any of the required input data sets are not found locally, the files that are missing will be listed. At this point, you must obtain the required data from the input data server using check_input_data with the -export option.
      • +
        +

      • The buildnml scripts in the various component cime_config directories create listings of required component input data sets in the Buildconf/$component.input_data_list files.

        +
        • +

      • check_input_data, which is called by case.build, checks for the presence of the required input data files in the root directory $DIN_LOC_ROOT.

        +
        • +

      • If all required data sets are found on the local disk, the build can proceed.

        +
        • +

      • If any of the required input data sets are not found locally, the files that are missing are listed. At this point, you must obtain the required data from the input data server with check_input_data as shown here:

        +
        check_input_data --export
+
        +
        +

      The env_run.xml variables $DIN_LOC_ROOT and $DIN_LOC_ROOT_CLMFORC determine where you should expect input data to reside on a local disk.

    diff --git a/users_guide/case-basics.html b/users_guide/case-basics.html index c18b6def94d..65d306b285b 100644 --- a/users_guide/case-basics.html +++ b/users_guide/case-basics.html @@ -99,17 +99,19 @@

    Quick search

    Two concepts to understand before working with CIME are component sets and model grids.

    • Component sets, which are usually referred to as “compsets,” define both individual model components and any component-specific namelist or configuration settings that are used in a case.
      • -
    • Model grids specify the grid or resolution for each component making up the model.
      • +
    • Model grids specify the grid or resolution for each component of the model.

    Creating a CIME experiment or case requires, at a minimum, specifying a compset and a model grid.

    -

    Out-of-the-box compsets and models grids are associated with two names: a longname and an alias name. Examples of both follow.

    -

    The CIME regression test system requires aliases, but aliases can also be used for convenience. Compset aliases are unique; each compset alias is associated with one and only one compset. Grid aliases, on the other hand, are overloaded; the same grid alias may result in a different grid depending on the associated compset. Always confirm that the compset longname and the grid longname are correct when using aliases to create a case.

    +

    Out-of-the-box compsets and models grids each have two names: a longname and an alias name. Examples of both follow.

    +

    The CIME regression test system requires aliases, but aliases can also be used for convenience. Compset aliases are unique; each is associated with one and only one compset. Grid aliases, on the other hand, are overloaded; the same grid alias may result in a different grid depending on the associated compset. Always confirm that the compset longname and the grid longname are correct when using aliases to create a case.

    2.1. Component sets

    A compset longname has this form:

    TIME_ATM[%phys]_LND[%phys]_ICE[%phys]_OCN[%phys]_ROF[%phys]_GLC[%phys]_WAV[%phys]_ESP[_BGC%phys]
-
-TIME = model time period (e.g. 1850, 2000, 20TR, RCP8...)
+
    +
    +

    Here are the supported values for each element of the longname:

    +
    TIME = model time period (e.g. 1850, 2000, 20TR, RCP8...)
 
 CIME supports the following values for ATM,LND,ICE,OCN,ROF,GLC,WAV and ESP.
 ATM  = [DATM, SATM, XATM]
@@ -144,23 +146,24 @@ 
    2.1. Component setsThe OPTIONAL %phys attributes specify sub-modes of the given system.
 For example, DOCN%DOM is the DOCN data ocean (rather than slab-ocean) mode.
 ALL the possible %phys choices for each component are listed by
-calling **manage_case** with the **-list** compsets argument.
+calling manage_case with the -list compsets argument.
 ALL data models have a %phys option that corresponds to the data model mode.
    -

    As an example, the CESM compset longname (below) refers to running a pre-industrial control with active CESM components CAM, CLM, CICE, POP2, MOSART, CISM2 and WW3 in a BDRD BGC coupling scenario.:

    +

    As an example, this actual CESM compset longname refers to running a pre-industrial control with active CESM components CAM, CLM, CICE, POP2, MOSART, CISM2 and WW3 in a BDRD BGC coupling scenario:

    1850_CAM60_CLM50%BGC_CICE_POP2%ECO_MOSART_CISM2%NOEVOLVE_WW3_BGC%BDRD
    -

    The alias for this compset is B1850. Input to create_newcase can be either a compset longname or a compset alias. -It is also possible to create your own custom compset. See How do I create my own compset? in the FAQ.

    +

    The alias for this compset is B1850. Either a compset longname or a compset alias can be input to create_newcase. You can also create your own custom compset. See How do I create my own compset? in the FAQ.

    2.2. Model Grids

    A model grid longname has the form:

    a%name_l%name_oi%name_r%name_m%mask_g%name_w%name
-
-a%  = atmosphere grid
+
    +
    +

    For reference:

    +
    a%  = atmosphere grid
 l%  = land grid
 oi% = ocean/sea-ice grid (must be the same)
 r%  = river grid
@@ -178,16 +181,16 @@ 
    2.2. Model Gridshowever, and is specified by the g% value.
    -

    As an example, examine this longname:

    +

    As an example, examine this actual grid longname:

    a%ne30np4_l%ne30np4_oi%gx1v7_r%r05_m%gx1v7_g%null_w%null
    -

    It refers to a model grid with a ne30np4 spectral element 1-degree atmosphere and land grids, gx1v7 Greenland pole 1-degree ocean and sea-ice grids, a 1/2 degree river routing grid, null wave and internal cism grids, and an gx1v7 ocean mask. +

    It refers to a model grid with a ne30np4 spectral element, 1-degree atmosphere and land grids, gx1v7 Greenland pole, 1-degree ocean and sea-ice grids, a 1/2 degree river routing grid, null wave and internal cism grids, and an gx1v7 ocean mask. The alias for this grid is ne30_g16.

    CIME also permits users to introduce their own user-defined grids.

    Component grids are denoted by the following naming convention:

    diff --git a/users_guide/cloning-a-case.html b/users_guide/cloning-a-case.html index 586ac7c8111..f84ddb78023 100644 --- a/users_guide/cloning-a-case.html +++ b/users_guide/cloning-a-case.html @@ -87,15 +87,15 @@

    Quick search

    8. Cloning a Case

    If you have access to a run that you want to clone, the create_clone command will create a new case while preserving local modifications to the case.

    -

    Here is the simplest example of using create_clone:

    -
    cd $CIMEROOT/scripts
-create_clone --case $CASEROOT --clone $CLONEROOT
+
    Here is a simple example:
    
+
    > cd $CIMEROOT/scripts
+> create_clone --case $CASEROOT --clone $CLONEROOT
 
    
 
    
 
    The create_clone script preserves any local namelist modifications made in the user_nl_xxxx files as well as any source code modifications in the SourceMods tree. Otherwise, $CASEROOT/ directory will appear as if create_newcase had just been run.
    
 
    Important: Do not change anything in the env_case.xml file.
    
 
    See the help text for more usage information.
    
-
    create_clone --help
+
    > create_clone --help
 
    
 
    
 
    Another approach to duplicating a case is to use the information in the case’s README.case and CaseStatus files to create a new case and duplicate the relevant xlmchange commands that were issued in the original case. This alternative will not preserve any local modifications that were made to the original case, such as source-code or build-script revisions; you will need to import those changes manually.
    
diff --git a/users_guide/create-a-case.html b/users_guide/create-a-case.html
index 4ed9fada083..3c15d0e1400 100644
--- a/users_guide/create-a-case.html
+++ b/users_guide/create-a-case.html
@@ -101,25 +101,36 @@ 
    Quick search
    
 
    3.1. Calling create_newcase
    
 
    The first step in creating a CIME-based experiment is to use create_newcase.
    
 
    If you are not on an out-of-the box CIME-supported platform, you will need to port CIME to your system before proceeding.
    
-
    Review the input options for create_newcase by using the —help option. The only required arguments to create_newcase are:
    
-
    create_newcase --case [CASE] --compset [COMPSET] --res [GRID]
+
    
+
    Review the input options for create_newcase in the  help text.
    
+
    > create_newcase --help
 
    
 
    
-
    CIME supports out of the box component sets, model grids* and hardware platforms. Compsets and grids were discussed in the previous section.
    
+
    
+
    The only required arguments to create_newcase are shown here:
    
+
    > create_newcase --case [CASE] --compset [COMPSET] --res [GRID]
+
    
+
    
+
    
+
    
+
    CIME supports out-of-the-box component sets, model grids and hardware platforms. Compsets and grids were discussed in the previous section.
    
 
    
 
    3.1.1. Result of calling create_newcase
    
 
    Following is a simple example of using create_newcase with aliases for both compset and grid names.
 The complete example appears in the basic example.
    
-
    In what follows, $CIMEROOT is the full pathname of the root directory of the CIME distribution.
    
-
    > cd $CIMEROOT/scripts
+
    
+
    Here, $CIMEROOT is the full pathname of the root directory of the CIME distribution.
    
+
    > cd $CIMEROOT/scripts
 > create_newcase --case ~/cime/example1 --compset A --res f09_g16_rx1
 
    
 
    
-
    In the example, the command creates a $CASEROOT directory ~/cime/example1. (If that directory already exists, a warning is printed and the command aborts.
    
+
    
+
    
+
    In the example, the command creates a $CASEROOT directory: ~/cime/example1. If that directory already exists, a warning is printed and the command aborts. Additional details:
    
 
      
-
    • $CASE is example1 ($CASE can include letters, numbers, ”.”, and “_”)
      • 
+
    • $CASE can include letters, numbers,  ”.”, and “_”. In the example, it is example1.
      • 
 
    • The compset is 2000_DATM%NYF_SLND_DICE%SSMI_DOCN%DOM_DROF%NYF_SGLC_SWAV.
      • 
-
    • The model resolution is a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%null_w%null
      • 
+
    • The model resolution is a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%null_w%null.
      • 
 
    • create_newcase installs files in $CASEROOT to build and run the model and to optionally archive the case on the target platform.
      • 
 
    
 
    Running create_newcase creates various scripts, files and directories $CASEROOT, as shown here.
    
@@ -133,37 +144,36 @@ 
    3.1.1. Result of calling create_newcase
 case.setup
-Script used to set up the case (create the case.run script, the Macros file and user_nl_xxx files)
+Script used to set up the case (create the case.run script, the Macros file and user_nl_xxx files).
 
 case.build
-Script to build component and utility libraries and model executable
+Script to build component and utility libraries and model executable.
 
 case.submit
-Script to submit the case to run using the machine’s batch queueing system
+Script to submit the case to run using the machine’s batch queueing system.
 
 case.st_archive
-Script to perform short-term archiving of output data
+Script to perform short-term archiving of output data.
 
 case.lt_archive
-Script to perform long-term archiving of output data
+Script to perform long-term archiving of output data.
 
 xmlchange
-Script to modify values in the xml files
+Script to modify values in the xml files.
 
 xmlquery
-Script to query values in the xml files
+Script to query values in the xml files.
 
 preview_namelists
-
    Script for users to see their component namelists in $CASEROOT/CaseDocs before running the model
    
-
    
+
    Script for users to see their component namelists in $CASEROOT/CaseDocs before running the model.
    
+
    
 
    Warning
    
-
    the namelists generated in $CASEROOT/CaseDocs should not be edited by the user
    
+
    Users should not edit namelists that are generated in $CASEROOT/CaseDocs. They are there only to document model behavior.
    
 
    
-
    they are only there to document model behavior.
    
 
 
 check_input_data
-Script for checking  for various input datasets and moves them into place.
+Script for checking for various input data sets and moving them into place.
 
 pelayout
 Script to query and modify the NTASKS, ROOTPE, and NTHRDS for each component model.  This a convenience script that can be used in place of xmlchange and xmlquery.
@@ -203,12 +213,11 @@ 
    3.1.1. Result of calling create_newcaseenv_run.xml
-
    Sets run-time settings such as length of run, frequency of restarts, output of coupler diagnostics,
    
-
    and short-term and long-term archiving.  This file can be edited at any time before a job starts.
    
-
+Sets runtime settings such as length of run, frequency of restarts, output of coupler diagnostics,
+and short-term and long-term archiving.  This file can be edited at any time before a job starts.
 
 env_batch.xml
-Sets batch system specific settings such as wallclock time and queue name.
+Sets batch system settings such as wallclock time and queue name.
 
 
 
@@ -223,7 +232,7 @@ 
    3.1.1. Result of calling create_newcase
 SourceMods
-Top-level directory containing sub-directories for each compset component where
+Top-level directory containing subdirectories for each compset component where
 you can place modified source code for that component.
 
 
@@ -257,14 +266,13 @@ 
    3.1.1. Result of calling create_newcase
 Buildconf/
-
    Work directory containing scripts to generate component namelists and component and utility libraries (e.g., PIO, MCT)
    
-
    You should never have to edit the contents of this directory.
    
-
+Work directory containing scripts to generate component namelists and component and utility libraries
+(PIO or MCT, for example). You should never have to edit the contents of this directory.
 
 LockedFiles/
 
    Work directory that holds copies of files that should not be changed.
    
 
    Certain xml files are locked after their variables have been used by should no longer be changed.
    
-
    CIME does this by locking a file and not permitting you to modify that file unless, depending on the file,                           case.setup —clean or  case.build —clean are called.
    
+
    CIME does this by locking a file and not permitting you to modify that file unless, depending on the file,                              case.setup --clean or  case.build --clean is called.
    
 
 
 Tools/
@@ -275,19 +283,19 @@ 
    3.1.1. Result of calling create_newcase$CASEROOT xml files are organized so that variables can be locked at certain points to prevent users from changing variables after they have been resolved (used) in other parts of the scripts system.
    
+
    The $CASEROOT xml files are organized so that variables can be locked at certain points to prevent users from changing them after they have been resolved (used) in other parts of the scripts system.
    
 
    CIME does the following:
    
 
      
 
    • Locks variables in env_case.xml after create_newcase.
      • 
-
    • Locks variables in env_mach_pes.xml are locked after case.setup.
      • 
+
    • Locks variables in env_mach_pes.xml after case.setup.
      • 
 
    • Locks variables in env_build.xml after completion of case.build.
      • 
 
    
 
    Variables in env_run.xml, env_batch.xml and env_archive.xml are never locked, and most can be changed at any time. There are some exceptions in the env_batch.xml file.
    
 
    The env_case.html file can never be unlocked.
    
-
    These files can be “unlocked” as follows:
    
+
    These other files can be “unlocked” as follows:
    
 
      
-
    • case.setup –clean unlocks env_mach_pes.xml
      • 
-
    • case.build –clean unlocks env_build.xml
      • 
+
    • To unlock env_mach_pes.xml, run case.setup --clean.
      • 
+
    • To unlock env_build.xml, run case.build --clean.
      • 
 
    
 
    
 
    
diff --git a/users_guide/introduction-and-overview.html b/users_guide/introduction-and-overview.html
index 7e2e9589147..12c403fff6e 100644
--- a/users_guide/introduction-and-overview.html
+++ b/users_guide/introduction-and-overview.html
@@ -99,37 +99,40 @@ 
    Quick search
    
             
   
    
 
    1. Introduction
    
-
    The Common Infrastructure for Modeling the Earth (CIME) provides a UNIX command-line-based user interface for
+
    The Common Infrastructure for Modeling the Earth (CIME) provides a UNIX command-line-based interface for
 configuring, compiling and executing Earth system models. Part 1 of this guide explains the basic commands
-needed to get a model running.
    
+that are needed to get a model running.
    
 
    
 
    1.1. Prerequisites
    
-
    Familiarity with the basic climate modeling concepts.
    
-
    Familiarity with UNIX command line terminals and the UNIX development environment.
    
-
    CIME’s commands are Python scripts and require a correct version of the Python interpreter to be installed.
    
-
    The Python version must be greater than 2.7 but less than 3.0. Determine which version you have by typing:
    
+
    Part 1 of this guide assumes that CIME and the necessary input files have been installed on
+the computer you are using. If that is not the case, see Installing CIME.
    
+
    Other prerequisites:
    
+
      
+
    • Familiarity with basic climate modeling concepts.
      • 
+
    • Familiarity with UNIX command line terminals and the UNIX development environment.
      • 
+
    • A correct version of the Python interpreter.
      • 
+
    
+
    CIME’s commands are Python scripts and require a correct version of the Python interpreter to be installed. The Python version must be greater than 2.7 but less than 3.0. Determine which version you have by typing:
    
 
    > python --version
 
    
 
    
-
    NOTE:  Part 1 of this guide assumes that CIME and the necessary input files have been installed on
-the computer you are using. If that is not the case, see Installing CIME.
    
 
    
 
    
 
    1.2. Terms and concepts
    
 
    The following terms and concepts are ingrained in CIME and are used frequently in this documentation.
    
 
    
-
    active vs data vs stub models:
    
-
    Components of a model that solve a complex set of equations to describe the model’s behavior are called
+
    active, data and stub models
    
+
    active models: Components of a model that solve a complex set of equations to describe the model’s behavior are called
 active models. Sometimes they are called prognostic or full models.
    
-
    CIME recognizes 7 different active models of a climate model. They are:
    
+
    CIME recognizes 7 different active models. They are:
    
 
    
 
    atmosphere, ocean, sea-ice, land surface, river, glacier, wave
    
 
    An external system processing (ESP) stub-only component is also allowed.
    
-
    For some climate problems, it is necessary to reduce feedbacks within the system by replacing an active model with a
+
    data models: For some climate problems, it is necessary to reduce feedbacks within the system by replacing an active model with a
 version that sends and receives the same variables to and from other models, but with the values read from files rather
 than computed from the equations. The values received are ignored. These active-model substitutes are called data models.
 CIME provides data models for each of the supported components.
    
-
    For some configurations, no data model is needed, so CIME provides stub versions that simply occupy the
+
    stub models: For some configurations, no data model is needed, so CIME provides stub versions that simply occupy the
 required place in the climate execution sequence and do not send or receive any data.
    
 
    
 
    case:
    
@@ -157,7 +160,7 @@ 
    1.2. Terms and concepts1.3. Setting defaults
    
 
    Before using any CIME commands, set the CIME_MODEL environment variable. In csh, use setenv as shown and replace
 <model> with the appropriate text, such as “acme” or “cesm.”
    
-
    setenv CIME_MODEL <model>
+
    > setenv CIME_MODEL <model>
 
    
 
    
 
    
@@ -285,14 +288,14 @@ 
    1.4. Directory content
 
    
 
    1.5. Discovering available cases
    
-
    To identify which compsets, grids and machines your CIME-enabled model supports, use the query_config command found in cime/scripts.  Use the —help option for more information.
    
+
    To identify which compsets, grids and machines your CIME-enabled model supports, use the query_config command found in cime/scripts.  See the help text for more information.
    
 
    > ./query_config --help
 
    
 
    
 
    
 
    
 
    1.6. Quick start
    
-
    To quickly see how a case is created, configured, built and run with CIME, execute the following commands for an example. (This assumes that CIME has been ported to your current machine).
    
+
    To see an example of how a case is created, configured, built and run with CIME, execute the following commands for an example. (This assumes that CIME has been ported to your current machine).
    
 
    > cd cime/scripts
 > ./create_newcase --case mycase --compset X --res f19_g16
 > cd mycase
@@ -302,11 +305,11 @@ 
    1.6. Quick start
    > tail CaseStatus
 
    
 
    
-
    Repeat the command until you see the message “case.run success”
    
+
    Repeat the command until you see the message case.run success.
    
 
    
 
    
 
diff --git a/users_guide/running-a-case.html b/users_guide/running-a-case.html
index 7bb1671e33a..f4f893bde9f 100644
--- a/users_guide/running-a-case.html
+++ b/users_guide/running-a-case.html
@@ -119,16 +119,14 @@ 
    Quick search
    
 
    6.1. Calling case.submit
    
 
    Before you submit the case using case.submit, make sure
 the batch queue variables are set correctly for your run
-targeted. The batch submissions variables are contained in the file
-$CASEROOT/env_batch.xml under the XML <group id="case.run">
-and <group id="case.st_archive"> elements. Make sure that you
-have appropriate account numbers (PROJECT), time limits
-(JOB_WALLCLOCK_TIME), and queue (JOB_QUEUE) for those groups..
    
-
    Also modify $CASEROOT/env_run.xml for your
-case using xmlchange.
    
-
    Once you have run case.setup and case.build, run
-case.submit to submit the run to your machine’s batch queue
-system.
    
+Those variables are contained in the file $CASEROOT/env_batch.xml
+under the XML <group id="case.run"> and <group id="case.st_archive">
+elements.
    
+
    Make sure that you have appropriate account numbers (PROJECT), time limits
+(JOB_WALLCLOCK_TIME), and queue (JOB_QUEUE) for those groups.
    
+
    Also modify $CASEROOT/env_run.xml for your case using xmlchange.
    
+
    Once you have executed case.setup and case.build, run case.submit
+to submit the run to your machine’s batch queue system.
    
 
    > cd $CASEROOT
 > ./case.submit
 
    
@@ -139,10 +137,10 @@ 
    6.1.1. Result of running case.submit
 
  • Load the necessary environment.
    • 
 
  • Confirm that locked files are consistent with the current xml files.
    • 
-
  • Run preview_namelist, which in turn will run each component’s buildnml
    • 
-
  • Run **check_input_data** to verify that the required
-data is present.
    • 
-
  • Submit the job to the batch queue. which in turn will run the script case.run.
    • 
+
  • Run preview_namelist, which in turn will run each component’s buildnml.
    • 
+
  • Run check_input_data to verify that the required
+data are present.
    • 
+
  • Submit the job to the batch queue. which in turn will run the case.run script.
    • 
 
 
    Upon successful completion of the run, case.run will:
    
 
 
    Short-term archiving will copy and move component history, log,
 diagnostic, and restart files from $RUNDIR to the short-term
-archive directory, $DOUT_S_ROOT.
    
+archive directory $DOUT_S_ROOT.
    
 
    
 
    
 
    6.1.2. Monitoring case job statuses
    
 
    The $CASEROOT/CaseStatus file contains a log of all the job states
-and xmlchange commands in chronological order. An example of status
-messages includes:
    
+and xmlchange commands in chronological order. Here is an example of status
+messages:
    
 
    2017-02-14 15:29:50: case.setup starting
 ---------------------------------------------------
 2017-02-14 15:29:54: case.setup success
@@ -184,8 +182,6 @@ 
    6.1.2. Monitoring case job statuses---------------------------------------------------
 
    
 
    
-
    When the short-term archiver is done, data from $RUNDIR is in
-subdirectories under $DOUT_S_ROOT.
    
 
    
 
    Note
    
 
    After a successful first run, set the env_run.xml variable
@@ -202,12 +198,12 @@ 
    6.1.2. Monitoring case job statuses
 
    6.1.3. Troubleshooting a job that fails
    
 
    There are several places to look for information if a job fails.
-Start with the STDOUT and STDERR file(s) in $CASEROOT.
+Start with the STDOUT and STDERR file(s) in $CASEROOT.
 If you don’t find an obvious error message there, the
 $RUNDIR/$model.log.$datestamp files will probably give you a
 hint.
    
-
    First check cpl.log.$datestamp, which will often tell you
-when the model failed. Then check the rest of the component log
+
    First, check cpl.log.$datestamp, which will often tell you
+when the model failed. Then check the rest of the component log
 files. See troubleshooting run-time
 problems for more information.
    
 
    
@@ -218,27 +214,26 @@ 
    6.1.3. Troubleshooting a job that fails$DIN_LOC_ROOT. It automatically downloads missing data.
    
 
    The required input data sets needed for each component are found in the
-$CASEROOT/Buildconf directory in the files xxx.input_data_list,
-where xxx is the component name. These files are generated by a call
+$CASEROOT/Buildconf directory. These files are generated by a call
 to preview_namlists and are in turn created by each component’s
 buildnml script. For example, for compsets consisting only of data
-models (that is, A compsets), the following files are created:
    
+models (A compsets), the following files are created:
    
 
    datm.input_data_list
 dice.input_data_list
 docn.input_data_list
 drof.input_data_list
 
    
 
    
-
    You can independently verify that the required data is present locally by
+
    You can independently verify the presence of the required data by
 using the following commands:
    
 
    > cd $CASEROOT
-> check_input_data -help
-> check_input_data -inputdata $DIN_LOC_ROOT -check
+> check_input_data --help
+> check_input_data --inputdata $DIN_LOC_ROOT --check
 
    
 
    
 
    If data sets are missing, obtain them from the input data server:
    
 
    > cd $CASEROOT
-> check_input_data -inputdata $DIN_LOC_ROOT -export
+> check_input_data --inputdata $DIN_LOC_ROOT --export
 
    
 
    
 
    
@@ -251,8 +246,20 @@ 
    6.1.3. Troubleshooting a job that fails$STOP_OPTION and
 $STOP_N. Other driver namelist settings then will have consistent and
-reasonable default values. These default settings guarantee that
+reasonable default values. The default settings guarantee that
 restart files are produced at the end of the model run.
    
+
    By default, the stop time settings are:
    
+
    STOP_OPTION = ndays
+STOP_N = 5
+STOP_DATE = -999
+
    
+
    
+
    The default settings are appropriate only for initial testing. Before
+starting a longer run, update the stop times based on the case
+throughput and batch queue limits. For example, if the model runs 5
+model years/day, set RESUBMIT=30, STOP_OPTION= nyears, and STOP_N=
+5. The model will then run in five-year increments and stop after
+30 submissions.
    
 
    
 
    6.3.1. Run-type initialization
    
 
    The case initialization type is set using the $RUN_TYPE variable in
@@ -298,8 +305,8 @@ 
    6.3.1. Run-type initializationhybrid
 
    A hybrid run is initialized like a startup but it uses
 initialization data sets from a previous case. It is similar
-somewhat analogous to a branch run with relaxed restart
-constraints. A hybrid run allows users to bring together
+to a branch run with relaxed restart  constraints.
+A hybrid run allows users to bring together
 combinations of initial/restart files from a previous case
 (specified by $RUN_REFCASE) at a given model output date
 (specified by $RUN_REFDATE). Unlike a branch run, the starting
@@ -323,25 +330,6 @@ 
    6.3.1. Run-type initialization$RUN_REFCASE and
 $RUN_REFDATE.  All run startup variables are discussed in
 `run start control variables<http://www.cesm.ucar.edu/models/cesm2.0/external-link-here>`_.
    
-
    A brief note on restarting runs
    
-
    When you first begin a branch, hybrid or startup run, CONTINUE_RUN
-must be set to FALSE. After the job has run successfully and
-there are restart files, you will need to change CONTINUE_RUN to
-TRUE for the remainder of your run. Setting the RESUBMIT option to
-a value > 0 will cause the CONTINUE_RUN variable to be set to TRUE
-automatically upon completion of the initial run.
    
-
    By default, the stop time settings are:
    
-
    STOP_OPTION = ndays
-STOP_N = 5
-STOP_DATE = -999
-
    
-
    
-
    The default settings are appropriate only for initial testing. Before
-starting a longer run, update the stop times based on the case
-throughput and batch queue limits. For example, if the model runs 5
-model years/day, set RESUBMIT=30, STOP_OPTION= nyears, and STOP_N=
-5. The model will then run in five-year increments, and stop after
-30 submissions.
    
 
    
 
    
 
    
@@ -349,27 +337,27 @@ 
    6.3.1. Run-type initialization$RUNDIR to a local disk area (short-term archiving).
 It has no impact on the production run except to clean up disk space
 in the $RUNDIR and help manage user quotas.
    
-
    In env_run.xml, several variables control the behavior of
+
    Several variables in env_run.xml control the behavior of
 short-term archiving. This is an example of how to control the
 data output flow with two variable settings:
    
 
    DOUT_S = TRUE
 DOUT_S_ROOT = /$SCRATCH/$user/$CASE/archive
 
    
 
    
-
    Key points to keep in mind about short-term archiving:
    
+
    The first setting above is the default, so short-term archiving is enabled. The second sets where to move files at the end of a successful run.
    
+
    Also:
    
 
      
-
    • Short-term archiving is enabled by default ($DOUT_S = TRUE).
      • 
 
    • All output data is initially written to $RUNDIR.
      • 
-
    • Unless a user explicitly turns off short-term archiving, files will
-be moved to $DOUT_S_ROOT at the end of a successful model run.
      • 
+
    • Unless you explicitly turn off short-term archiving, files are
+moved to $DOUT_S_ROOT at the end of a successful model run.
      • 
 
    • Users generally should turn off short-term archiving when developing new code.
      • 
 
    
 
    Standard output generated from each component is saved in $RUNDIR
@@ -400,24 +388,21 @@ 
    6.3.1. Run-type initialization
 
    6.5. Restarting a run
    
-
    Each active component (and some data components) write restart files
+
    Active components (and some data components) write restart files
 at intervals that are dictated by the driver via the setting of the
 $REST_OPTION and $REST_N variables in env_run.xml. Restart
 files allow the model to stop and then start again with bit-for-bit
 exact capability; the model output is exactly the same as if the model
-had not stopped). The driver coordinates the writing of restart
-files as well as the time evolution of the model. All components
-receive restart and stop information from the driver and write
-restarts or stop as the drives specifies.
    
-
    Keep in mind that runs initialized as branch or hybrid runs, require
+had not stopped. The driver coordinates the writing of restart
+files as well as the time evolution of the model.
    
+
    Runs that are initialized as branch or hybrid runs require
 restart/initial files from previous model runs (as specified by the
-variables $RUN_REFCASE and $RUN_REFDATE). The user must pre-stage
-these required files to the case $RUNDIR (normally $EXEROOT/run)
+variables $RUN_REFCASE and $RUN_REFDATE). Pre-stage these
+iles to the case $RUNDIR (normally $EXEROOT/run)
 before the model run starts. Normally this is done by copying the contents
 of the relevant $RUN_REFCASE/rest/$RUN_REFDATE.00000 directory.
    
 
    Whenever a component writes a restart file, it also writes a restart
-pointer file in the format rpointer.$component. The pointer
-file contains the name of that new restart file. Upon a restart, each
+pointer file in the format rpointer.$component. Upon a restart, each
 component reads the pointer file to determine which file to read in
 order to continue the run. These are examples of pointer files created
 for a component set using full active model components.
    
@@ -441,13 +426,13 @@ 
    6.5.1. Backing up to a previous restart$RUNDIR).
    
-
    Make sure that the new rpointer.* files overwrite older files in
-in $RUNDIR, or the job may not restart in the correct place.
    
-
    You can then continue the run using the new restarts.
    
+
    Make sure that the new restart pointer files overwrite older files in
+in $RUNDIR or the job may not restart in the correct place. You can
+then continue the run using the new restarts.
    
 
    Occasionally, when a run has problems restarting, it is because the
-rpointer.* and restart files are out of sync. The rpointer.* files
-are text files that can easily be edited to match the correct dates
-of the restart and history files. All the restart files should
+pointer and restart files are out of sync. The pointer files
+are text files that can be edited to match the correct dates
+of the restart and history files. All of the restart files should
 have the same date.
    
 
    
 
    
@@ -458,8 +443,7 @@ 
    6.6. Archiving model output data$RUNDIR directory.
    
 
    The output data flow from a successful run depends on whether or not
-short-term archiving is enabled, as it is by default. (The env_run.xml
-variable $DOUT_S is set as DOUT_S=TRUE.
    
+short-term archiving is enabled, as it is by default.
    
 
    
 
    6.6.1. No archiving
    
 
    If no short-term archiving is performed, model output data remains
diff --git a/users_guide/setting-up-a-case.html b/users_guide/setting-up-a-case.html
index b82e6c1a479..ede74dfa2e2 100644
--- a/users_guide/setting-up-a-case.html
+++ b/users_guide/setting-up-a-case.html
@@ -96,8 +96,7 @@ 
    Quick search
    
 
    4. Setting up a Case
    
 
    
 
    4.1. Calling case.setup
    
-
    After creating a case or changing aspects of a case, such as the pe-layout, call the case.setup command from $CASEROOT This creates additional files and directories in $CASEROOT. They are described below.
    
-
    To see the options that are available with case.setup, use the —help. option.
    
+
    After creating a case or changing aspects of a case, such as the pe-layout, call the case.setup command from $CASEROOT. This creates additional files and directories in $CASEROOT. They are described below.
    
 
    
 
    @@ -106,29 +105,27 @@ 
    4.1. Calling case.setup
 
    
-
+
-
diff --git a/users_guide/troubleshooting.html b/users_guide/troubleshooting.html
index aeb33ed6c61..19fd5b06725 100644
--- a/users_guide/troubleshooting.html
+++ b/users_guide/troubleshooting.html
@@ -100,7 +100,7 @@ 
    Quick search
    
 
    9.1. Troubleshooting case creation
    Generally, create_newcase errors are reported to the terminal and should provide some guidance about what caused them.
    If create_newcase fails on a relatively generic error, first check to make sure the command-line arguments match the interface’s specification. See the help text to review usage.
    
-
    create_newcase --help
+
    > create_newcase --help
 
    
 
    
 
    
@@ -117,7 +117,7 @@ 
    9.2. Troubleshooting job submission
 
    9.3. Troubleshooting runtime problems
    
 
    To see if a run completed successfully, check the last several lines of the cpl.log file for a string like SUCCESSFUL TERMINATION. A successful job also usually copies the log files to the $CASEROOT/logs directory.
    
-
    Note: The first things to check when a job fails:
    
+
    Check these things first when a job fails:
    
 
 
    Common errors
    
 
    One common error is for a job to time out, which often produces minimal error messages.
@@ -147,7 +146,7 @@ 
    9.3. Troubleshooting runtime problemstStamp as shown here:
    
-
    grep tStamp cpl.log.* | more
+
    > grep tStamp cpl.log.* | more
 
    
 
    
 
    The output looks like this:
    
@@ -167,7 +166,7 @@ 
    9.3. Troubleshooting runtime problemsrestarting a run.
    
+See Restarting a run.
    
 
    It is not uncommon for nodes to fail on HPC systems or for access to large file systems to hang. Before you file a bug report, make sure a case fails consistently in the same place.
    
 
    
 
    

    
 

    case.run
    Run script containing the batch directives
    
-
    The batch directives are generated using the contents of env_mach_pes.xml.
-Calling case.setup –clean will remove this file.
    
-    		Run script containing the batch directives. The directives are generated using the contents
+of env_mach_pes.xml. Running case.setup --clean will remove this file.
 
    
 
    Macros.make
    File containing machine-specific makefile directives for your target platform/compiler.
    
-
    This file is created if it does not already exist.
    
-
    The user can modify this file to change certain aspects of the build, such as compiler flags.
    
-
    Calling case.setup –clean will not remove the file once it has been created.
-However. if you remove or rename the Macros.make file, case.setup will recreate it.
    
+
    File containing machine-specific makefile directives for your target platform/compiler.
+This file is created if it does not already exist.
    
+
    The user can modify the file to change certain aspects of the build, such as compiler flags.
+Running case.setup --clean will not remove the file once it has been created.
+However. if you remove or rename the Macros.make file, running case.setup recreates it.
    
     		
 
    
 
    user_nl_xxx[_NNNN] files
 
    Files where all user modifications to component namelists are made.
    
 
    xxx is any one of the set of components targeted for the case.
-For example, for a full active CESM compset, xxx would be cam, clm, rtm, and so on.
    
+For example, for a full active CESM compset, xxx is cam, clm or rtm, and so on.
    
 
    NNNN goes from 0001 to the number of instances of that component.
 (See multiple instances)
    
 
    For a case with 1 instance of each component (default), NNNN will not appear
 in the user_nl file names.
    
-
    A user_nl file of a given name will only be created once.
    
-
    Calling case.setup –clean will not remove any user_nl files.
    
+
    A user_nl file of a given name is created only once.
    
+
    Calling case.setup --clean will not remove any user_nl files.
    
 
    Changing the number of instances in the env_mach_pes.xml file will cause only
 new user_nl files to be added to $CASEROOT.