Heracles 4.0 User's Guide: Difference between revisions
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=== Using <code>gcm_setup</code> === | === Using <code>gcm_setup</code> === | ||
The setup script for global runs, <code>gcm_setup</code>, is in the directory <code>src/Applications/GEOSgcm_App</code>. The following is an example of a session with the setup script, with commentary. : | The setup script for global runs, <code>gcm_setup</code>, is in the directory <code>src/Applications/GEOSgcm_App</code>. The following is an example of a session with the setup script, with commentary. : | ||
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Enter the Experiment ID: | Enter the Experiment ID: | ||
Enter a name and hit return. For this example we'll set the experiment ID to "myexp42". Experiment IDs need to have no whitespace and not start with a digit, since it will be the prefix of job names and the queue system imposes certain limits on job names. | Enter a name and hit return. For this example we'll set the experiment ID to "myexp42". Experiment IDs need to have no whitespace and not start with a digit, since it will be the prefix of job names and the queue system imposes certain limits on job names. | ||
Enter a 1-line Experiment Description: | |||
Enter a 1-line Experiment Description: | |||
This should be short but descriptive, since it will be used to label plots. It can have spaces, though the string will be stored with underscores for the spaces. Provide a description and hit return. | This should be short but descriptive, since it will be used to label plots. It can have spaces, though the string will be stored with underscores for the spaces. Provide a description and hit return. | ||
Enter an Experiment Source Tag for History (Default: Heracles-4_0): | |||
The setup script extracts the repository tag of the model you checked out into your sandbox, checks out that tag from the repository, and creates a tarball of the source tree to keep with the experiment. It also <code>diff</code>s your sandbox against the tag it checks out and records those differences with the tarball in <code><i>EXPDIR</i>/src</code>. This is where you can change the default tag extracted from your sandbox. | |||
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This gives you an opportunity to copy the setup of an existing experiment while changing what needs to be changed to make it work. | |||
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The options b/c/d/e select a resolution with lat/lon, and c48-c1440 select one with the cubed sphere. Enter a resolution like so: | The options b/c/d/e select a resolution with lat/lon, and c48-c1440 select one with the cubed sphere. Enter a resolution like so: | ||
c48 | |||
c48 | |||
and hit enter. | and hit enter. | ||
Enter the Atmospheric Model Vertical Resolution: LM (Default: 72) | |||
Do you wish to run the COUPLED Ocean/Sea-Ice Model? (Default: NO or FALSE) | |||
Do you wish to run the COUPLED Ocean/Sea-Ice Model? (Default: NO or FALSE) | |||
You probably don't, so hit enter. | You probably don't, so hit enter. | ||
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Unless you are using a higher-resolution experiment, the default will suffice. | Unless you are using a higher-resolution experiment, the default will suffice. | ||
Do you wish to run GOCART? (Default: NO or FALSE) | |||
Do you wish to run GOCART? (Default: NO or FALSE) | |||
GOCART is the interactive chemistry package, as opposed to prescribed chemistry. It incurs a significant performance cost, so unless you know you want it, you should go with the default. The following assumes that you have entered "y". Otherwise, skip two steps to "Enter the tag..." | GOCART is the interactive chemistry package, as opposed to prescribed chemistry. It incurs a significant performance cost, so unless you know you want it, you should go with the default. The following assumes that you have entered "y". Otherwise, skip two steps to "Enter the tag..." | ||
Enter the GOCART Emission Files to use: MERRA2 (Default), PIESA, CMIP, NR, MERRA2-DD or OPS: | |||
Select your favorite emission files here. | Select your favorite emission files here. | ||
Enter the AERO_PROVIDER: GOCART (Default) or GOCART.data: | |||
Enter the AERO_PROVIDER: GOCART (Default) or | |||
Here you get to choose again to use interactive or prescribed aerosols. | Here you get to choose again to use interactive or prescribed aerosols. | ||
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This provides a default HISTORY.rc (output specification) file. The initial default will be the tag of the build in which you are running <code>gcm_setup</code>. The idea is that you can save a custom <code>HISTORY.rc</code> to the repository and have it checked out for your experiments. | This provides a default HISTORY.rc (output specification) file. The initial default will be the tag of the build in which you are running <code>gcm_setup</code>. The idea is that you can save a custom <code>HISTORY.rc</code> to the repository and have it checked out for your experiments. | ||
Enter Desired Location for HOME Directory (to contain scripts and RC files) | |||
Hit ENTER to use Default Location: | |||
Enter Desired Location for HOME Directory (to contain scripts and RC files) | ---------------------------------- | ||
Hit ENTER to use Default Location: | Default: /discover/nobackup/aeichman/myexp42 | ||
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Default: /discover/nobackup/aeichman/myexp42 | |||
This option determines where the experiment's home directory is located -- where the basic job scripts and major RC files (<code>AGCM.rc</code>, <code>CAP.rc</code> and <code>HISTORY.rc</code>) will be located. The first time you run the script it will default to a subdirectory under your account's home directory named <code>geos5</code>, remember what you decide (in <code>~/.HOMDIRroot</code>) and use that as a default in subsequent times the script is run. This initial default is fine, though another possibility is to enter your nobackup space, as shown here. This will place all of the HOME directory files of the experiment together with the rest of them. | This option determines where the experiment's home directory is located -- where the basic job scripts and major RC files (<code>AGCM.rc</code>, <code>CAP.rc</code> and <code>HISTORY.rc</code>) will be located. The first time you run the script it will default to a subdirectory under your account's home directory named <code>geos5</code>, remember what you decide (in <code>~/.HOMDIRroot</code>) and use that as a default in subsequent times the script is run. This initial default is fine, though another possibility is to enter your nobackup space, as shown here. This will place all of the HOME directory files of the experiment together with the rest of them. | ||
Enter Desired Location for EXPERIMENT Directory (to contain model output and restart files) | |||
Enter Desired Location for EXPERIMENT Directory (to contain model output and restart files) | Hit ENTER to use Default Location: | ||
Hit ENTER to use Default Location: | ---------------------------------- | ||
---------------------------------- | Default: /discover/nobackup/aeichman/myexp42 | ||
Default: /discover/nobackup/aeichman/myexp42 | |||
This determines the experiment directory, where restart files and various job output is stored. These are the storage-intensive parts and so default to the <code>nobackup</code> space. | This determines the experiment directory, where restart files and various job output is stored. These are the storage-intensive parts and so default to the <code>nobackup</code> space. | ||
Enter Location for Build directory containing: src/ Linux/ etc... | Enter Location for Build directory containing: src/ Linux/ etc... | ||
Hit ENTER to use Default Location: | Hit ENTER to use Default Location: | ||
---------------------------------- | ---------------------------------- | ||
Default: /discover/nobackup/aeichman/Heracles-4_0 | Default: /discover/nobackup/aeichman/Heracles-4_0 | ||
This determines which of your local builds is used to create the experiment. It defaults to the build of the script you are running, which is generally a good idea. | This determines which of your local builds is used to create the experiment. It defaults to the build of the script you are running, which is generally a good idea. | ||
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Creating gcm_convert.j for Experiment: myexp42 | Creating gcm_convert.j for Experiment: myexp42 | ||
Creating gcm_plot.tmpl for Experiment: myexp42 | Creating gcm_plot.tmpl for Experiment: myexp42 | ||
Creating gcm_quickplot.csh for Experiment: myexp | |||
Creating gcm_moveplot.j for Experiment: myexp | |||
Creating gcm_stats.j for Experiment: myexp | |||
Creating gcm_forecast.tmpl for Experiment: myexp42 | Creating gcm_forecast.tmpl for Experiment: myexp42 | ||
Creating gcm_forecast.setup for Experiment: myexp42 | Creating gcm_forecast.setup for Experiment: myexp42 | ||
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=== Using restart files === | === Using restart files === | ||
Restart files provide the initial conditions for a run, and a set needs to be copied into a fresh experiment directory before running. This includes the file <code>cap_restart</code>, which provides the model starting date and time in text. Restart files themselves are resolution-specific and sometimes change between model versions. As of the current model version, they are flat binary files | Restart files provide the initial conditions for a run, and a set needs to be copied into a fresh experiment directory before running. This includes the file <code>cap_restart</code>, which provides the model starting date and time in text. Restart files themselves are resolution-specific and sometimes change between model versions. As of the current model version, they are now netcdf files with metadata instead of the previous flat binary files but typically have the same naming convention, so they tend to be stored together with restarts of the same provinance with the date either embedded in the filename or in an accompanying <code>cap_restart</code>, typically under a directory indicating the model version. If you have restarts from a previous model version it may be worthwhile to try running with them as the model will check to see if they are in netcdf format, and if not, convert them. | ||
A cleanly completed model run will leave a set of restarts and the corresponding <code>cap_restart</code> in its experiment directory. Another source is <code>/archive/u/aeichman/restarts</code>. Restarts are also left during runs in date-labeled tarballs in the <code>restarts</code> directory under the experiment directory before being transferred to the user's <code>/archive</code> space. You may have to create the <code>cap_restart</code>, which is simply one line of text with the date of the restart files in the format ''YYYYMMDD HHMMSS'' (with a space). | A cleanly completed model run will leave a set of restarts and the corresponding <code>cap_restart</code> in its experiment directory. Another source is <code>/archive/u/aeichman/restarts</code>. Restarts are also left during runs in date-labeled tarballs in the <code>restarts</code> directory under the experiment directory before being transferred to the user's <code>/archive</code> space. You may have to create the <code>cap_restart</code>, which is simply one line of text with the date of the restart files in the format ''YYYYMMDD HHMMSS'' (with a space). | ||
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Setting <code>PRINTSPEC</code> to 3 will make the model send to standard output a list of exports available to <code>HISTORY.rc</code> in the model's current configuration, and then exit without integrating. The list includes each export's gridded component and short name (both necessary to include in <code>HISTORY.rc</code>), long (descriptive) name, units, and number of dimensions. Note that run-time options can affect the exports available, so see to it that you have those set as you intend. The other <code>PRINTSPEC</code> values are useful for debugging. | Setting <code>PRINTSPEC</code> to 3 will make the model send to standard output a list of exports available to <code>HISTORY.rc</code> in the model's current configuration, and then exit without integrating. The list includes each export's gridded component and short name (both necessary to include in <code>HISTORY.rc</code>), long (descriptive) name, units, and number of dimensions. Note that run-time options can affect the exports available, so see to it that you have those set as you intend. The other <code>PRINTSPEC</code> values are useful for debugging. | ||
While you can set <code>PRINTSPEC</code>, submit <code> | While you can set <code>PRINTSPEC</code>, submit <code>sbatch gcm_run.j</code>, and get the export list as part of PBS standard output, there are quicker ways of obtaining the list. One way is to run it as a single column model on a single processor, as explained in [[Heracles 4.0 Single Column Model]]. Another way is to run it in an existing experiment. In the <code>scratch</code> directory of an experiment that has already run, change <code>PRINTSPEC</code> in <code>CAP.rc</code> as above. Then, in the file <code>AGCM.rc</code>, change the values of <code>NX</code> and <code>NY</code> (near the beginning of the file) to 1. Then, from an interactive job (one processor will suffice), run the executable <code>GEOSgcm.x</code> in <code>scratch</code>. You will need to run <code>source src/g5_modules</code> in the model's build tree to set up the environment. The model executable will simply output the export list to <code>stdout</code>. | ||
===Outputting Derived Fields=== | ===Outputting Derived Fields=== | ||