Running E3SM: step-by-step guide

Contact: @Ryan Forsyth


  • Useful Aliases

    • The aliases provided in this section may be useful.

  • Configuring the Model Run – Run Script

    • The run-script remains mostly the same between runs. Users can change configuration parameters in it though.

  • Running the Model

    • It is recommended to run a few short tests before starting a production simulation.

  • Short Term Archiving

    • To avoid having so many output files in one directory, we can archive output into appropriate subdirectories.

  • Performance Information

    • PACE is used to display performance information from a run.

  • Re-Submitting a Job After a Crash

    • If a job crashes, it is easy to re-submit after making a fix.

  • Post-Processing with zppy

    • zppy is a tool that brings multiple post-processing tools together – with zppy, users can easily run E3SM Diags and MPAS-Analysis as well as generate global time series plots.

  • Documenting the Model Run

    • Model runs should be documented on its own Confluence page providing run details and results.

  • Long Term Archiving with zstash

    • zstash can be used to archive results for the long-term.

  • Publishing the simulation data (Optional)


Useful Aliases

Setting some aliases may be useful in running the model. You can edit ~/.bashrc to add aliases. Run source ~/.bashrc to start using them.

Note that the specific file name may differ amongst machines. Other possibilities include ~/.bash_profile, ~/.bashrc.ext, or ~/.bash_profile.ext.

Batch jobs

To check on all batch jobs:

alias sqa='squeue -o "%8u %.7a %.4D %.9P %7i %.2t %.10r %.10M %.10l %.8Q %j" --sort=P,-t,-p'

To check on your batch jobs:

alias sq='sqa -u $USER'

The output of sq uses several abbreviations: ST = Status, R = running, PD = pending, CG = completing.


You will be working in several directories.

On anvil or chrysalis (i.e., LCRC machines), those paths are:

<run_scripts_dir>: ${HOME}/E3SM/scripts

<code_source_dir>: ${HOME}/E3SM/code

<simulations_dir>: /lcrc/group/e3sm/<username>/E3SMv2

So, it may be useful to set the following aliases:

# Model running alias run_scripts="cd ${HOME}/E3SM/scripts/" alias simulations="cd /lcrc/group/e3sm/<username>/E3SMv2/"

On other machines, the paths are the same, except for the <simulations_dir>.

On compy (PNNL):

<simulations_dir>: /compyfs/<username>/E3SMv2

On cori (NERSC):

<simulations_dir>: ${CSCRATCH}/E3SMv2

Configuring the Model Run – Run Script

Start with an example of a run script for a low-resolution coupled simulation:

Create a new run script or copy an existing one. The path to it should be <run_scripts_dir>/run.<case_name>.sh

# Machine and project

  • readonly MACHINE=chrysalis: the name of the machine you’re running on.

  • readonly PROJECT="e3sm": SLURM project accounting (typically e3sm).

# Simulation

  • readonly COMPSET="WCYCL1850" : compset (configuration)

  • readonly RESOLUTION="ne30pg2_EC30to60E2r2": resolution (low-resolution coupled simulation in this case)

    • ne30 is the number of spectral elements for the atmospheric dynamics grid, while pg2 refers to the physics grid option. This mesh grid spacing is approximately 110 km.

    • EC30to60E2r2 is the ocean and sea-ice resolution. The grid spacing varies between 30 and 60 km.

    • For simulations with regionally refined meshes such as the N American atmosphere grid coupled to the WC14 ocean and sea-ice, replace with northamericax4v1pg2_WC14to60E2r3.

  • readonly CASE_NAME="v2.LR.piControl":

    • v2.LR is a short custom description to help identify the simulation.

    • piControl is the type of simulation. Other options here include , but are not limited to: amip, F2010.

  • readonly CASE_GROUP="v2.LR":

    • This will let you mark multiple cases as part of the same group for later processing (e.g., with PACE).

    • Note: If this is part of a simulation campaign, ask your group lead about using a case_group label. Otherwise, please use a unique name to distinguish from existing case_group label names, i.g. “v2.LR“.

# Code and compilation

  • readonly CHECKOUT="20210702": date the code was checked out on in the form {year}{month}{day}. The source code will be checked out in sub-directory named {year}{month}{day} under <code_source_dir>.

  • readonly BRANCH="master": branch the code was checked out from. Valid options include “master”, a branch name, or a git hash. For provenance purposes, it is best to specify the git hash.

  • readonly DEBUG_COMPILE=false : option to compile with DEBUG flag (leave set to false)

# Run options

  • readonly MODEL_START_TYPE="hybrid" : specify how the model should start – use initial conditions, continue from existing restart files, branch, or hybrid.

  • readonly START_DATE="0001-01-01" : model start date. Typically year 1 for simulations with perpetual (time invariant) forcing or a real year for simulation for transient forcings.

# Set paths

  • readonly CODE_ROOT="${HOME}/E3SMv2/code/${CHECKOUT}": where the E3SM code will be checked out.

  • readonly CASE_ROOT="/lcrc/group/e3sm/${USER}/E3SMv2/${CASE_NAME}": where the results will go. The directory ${CASE_NAME} will be in <simulations_dir>.

# Sub-directories

  • readonly CASE_BUILD_DIR=${CASE_ROOT}/build : all the compilation files, including the executable.

  • readonly CASE_ARCHIVE_DIR=${CASE_ROOT}/archive : where short-term archived files will reside.

# Define type of run

  • readonly run='production': type of simulation to run – i.e, a short test for verification or a long production run. (See next section for details).

# Coupler history

  • readonly HIST_OPTION="nyears"

  • readonly HIST_N="5"

# Leave empty (unless you understand what it does)

  • readonly OLD_EXECUTABLE="" : this is a somewhat risky option that allows you to re-use a pre-existing executable. This is not recommended because it breaks provenance.

# --- Toggle flags for what to do ----

This section controls what operations the script should perform. The run-e3sm script can be invoked multiple times with the user having the option to bypass certain steps by toggling true / false

  • do_fetch_code=false : fetch the source code from Github.

  • do_create_newcase=true : create new case.

  • do_case_setup=true : case setup.

  • do_case_build=false : compile.

  • do_case_submit=true : submit simulation.

The first time the script is called, all the flags should be set to true. Subsequently, the user may decide to bypass code checkout (do_fetch_code=false) or compilation (do_case_build=false). A user may also prefer to manually submit the job by setting do_case_submit=false and then invoking ./case.submit.


A case is tied to one code base and one executable. That is, if you change CHECKOUT or BRANCH, then you should also change CASE_NAME.

Running the Model

Short tests

Before starting a long production run, it is highly recommended to perform a few short tests to verify:

  1. The model starts without errors.

  2. The model produces BFB (bit-for-bit) results after a restart.

  3. The model produces BFB results when changing PE layout.

(1) can spare you from a considerable amount of frustration. Imagine submitting a large job on a Friday afternoon, only to discover Monday morning that the job started to run on Friday evening and died within seconds because of a typo in a namelist variable or input file.

Many code bugs can be caught with (2) and (3). While the E3SM nightly tests should catch such non-BFB errors, it is possible that you’ll be running a slightly different configuration (for example a different physics option) for which those tests have not been performed.

Running short tests

The type of run to perform is controlled by the script variable run.

You should typically perform at least two short tests (two different layouts, with and without restart).

First, let’s start with a short test using the 'S' (small) PE layout and running for 2x5 days:

  • readonly run='S_2x5_ndays'

If you have not fetched and compiled the code, set all the toggle flags to true:

do_fetch_code=true do_create_newcase=true do_case_setup=true do_case_build=true do_case_submit=true

At this point, execute the run-e3sm script:

cd <run_scripts_dir> ./run.<case_name>.sh

Fetching the code and compiling it will take some time (30 to 45 minutes), so go ahead a brew yourself a fresh cup of coffee. Once the script finished, the test job will have been submitted to the batch queue.

You can immediately edit the script to prepare for the second short test. In this case, we will be running for 10 days (without restart) using the 'M' (medium PE layout):

  • readonly run='M_1x10_ndays'

Since the code has already been fetched and compiled, change the toggle flags:

and execute the script

Since we are bypassing the code fetch and compilation (by re-using the previous executable), the script should only take a few seconds to run and again should submit the second test.

Note that short tests use separate output directories, so it is safe to submit and run multiple tests at once. If you’d like, you could submit additional test, for example 10 days with the medium 80 nodes ('M80') layout (M80_1x10_ndays).

Verifying results are BFB

Once the short tests are complete, we can confirm the results were bit-for-bit (BFB) the same. All the test output is located under the tests sub-directory:

To verify that the results are indeed BFB, we extract global integral from the atmosphere log files (lines starting with ‘nstep, te’) and make sure that they are identical for all tests.

If the BFB check fails, you should stop here and understand why. If they succeed, you can now start the production simulation.

Production simulation

To prepare for the long production simulation, edit the run e3sm script and set:

  • readonly run='production'

In addition, you may need to customize the code block below that some variables in the code block below to configure run options:

# Production simulation

  • readonly PELAYOUT="M": 1=single processor, S=small, M=medium, L=large, X1=very large, X2=very very large. Production simulations typically use M or L. The size determines how many nodes will be used. The exact number of nodes will differ amongst machines.

  • readonly WALLTIME="28:00:00" : maximum wall clock time requested for the batch jobs.

  • readonly STOP_OPTION="nyears"

  • readonly STOP_N="20" : units and length of each segment (i.e. each batch job)

  • readonly REST_OPTION="nyears"

  • readonly REST_N="5" : units and frequency for writing restart files (make sure STOP_N is a multiple of REST_N, otherwise the model will stop without writing a restart fie at the end).

  • readonly RESUBMIT=”9” : number of resubmissions beyond the original segment. This simulation would run for a total of 200 years (20 + 9x20).

  • readonly DO_SHORT_TERM_ARCHIVING=false : leave set to false if you want to manually run the short term archive.

Since the code has already been fetched and compiled for the short tests, the toggle flags can be set to:

Finally, execute the script

The script will automatically submit the first job. New jobs will be automatically be resubmitted at the end until the total number of segments have been run.

Looking at Results

Explanation of directories:

  • build: all the stuff to compile. The executable (e3sm.exe) is also there.

  • case_scripts: the files for your particular simulation.

  • run: where all the output will be. Most components (atmosphere, ocean, etc.) have their own log files. The coupler exchanges information between the components. The top level log file will be of the form run/e3sm.log.*. Log prefixes correspond to components of the model:

    • atm: atmosphere

    • cpl: coupler

    • ice: sea ice

    • lnd: land

    • ocn: ocean

    • rof: river runoff

Run tail -f run/<component>.log.<latest log file> to keep up with a log in real time.

You can use the sq alias defined in the “Useful Aliases” section to check on the status of the job. The NODE in the output indicates the number of nodes used and is dependent on the processor_config / PELAYOUTsize.

When running on two different machines (such as Compy and Chrysalis) and/or two different compilers, the answers will not be the same, bit-for-bit. It is not possible using floating point operations to get bit-or-bit identical results across machines/compilers.

Logs being compressed to .gz files is one of the last steps before the job is done and will indicate successful completion of the segment. less <log>.gz will let you directly look at a gzipped log.

Short Term Archiving

By default, E3SM will store all output files under the run/ sub-directory. For long simulations, there could 10,000s to 100,000s of output files. Having so many files in a single directory can be very impractical, slowing down simple operations like ls to a crawl. CIME includes a short-term archiving utility that will neatly organize output files into a separate archive/ sub-directory.

Short term archiving can be accomplished with the following steps. This can be done while the model is still running.

Use --force-move to move instead of copying, which can take a long time. Set --last-date to the latest date in the simulation you want to archive. You do not have to specify a beginning date.

Each component of the model has a subdirectory in archive. There are also two additional subdirectories: logs holds the gzipped log files and rest holds the restart files.



Files in the Subdirectory



Files in the Subdirectory

Atmosphere (Earth Atmospheric Model)






Sea Ice (MPAS-Sea-Ice)



Land (Earth Land Model)



Ocean (MPAS-Ocean)



River Runoff (MOSART)




Performance Information

Model throughput is the number of simulated years per day. You can find this with:

PACE provides detailed performance information. Go to and enter your username to search for your jobs. You can also simply search by providing the JobID appended to log files (NNNNN.yymmdd-hhmmss where NNNNN is the Slurm job id). Click on a job ID to see its performance details. “Experiment Details” are listed at the top of the job’s page. There is also a helpful chart detailing how many processors and how much time each component (atm, ocn, etc.) used. White areas indicate time spent idle/waiting. The area of each box is essentially the "cost = simulation time * number of processors" of the corresponding component.

Re-Submitting a Job After a Crash

If a job crashes, you can rerun with:

If you need to change a XML value, the following commands in the case_scripts directory are useful:

Before re-submitting:

  • Check that the rpointer files all point to the last restart. On very rare occasions, there might be some inconsistency if the model crashed at the end.

    • Run head -n 1 rpointer.* to see the restart date.

  • gzip all the *.log files from the faulty segment so that they get moved during the next short-term archiving. To gzip log files from failed jobs, run gzip *.log.<job ID>* (where <job ID> has no periods/dots in it).

  • Delete core or error files if there are any. MPAS components will sometimes produce a large number of them. The following commands are useful for checking for these files:

    • ls | grep -in core

    • ls | grep -in err

  • If you are re-submitting the initial job, you will need to run ./xmlchange -id CONTINUE_RUN -val TRUE

Post-Processing with zppy

To post-process a model run, do the following steps. Note that to post-process up to year n, then you must have short-term archived up to year n.

You can ask questions about zppy on

Install zppy

Load the E3SM unified environment. For Chrysalis, this is: source /lcrc/soft/climate/e3sm-unified/ Commands for other machines, and installation guide for development version of zppy can be found at

Configuration File

Create a new post-processing configuration file or copy an existing one. A good starting point is the configuration file corresponding to the simulation above: (Note: this is a private repo)

Call it post.<case_name>.cfg and place it in your <run_scripts_dir>.

Edit the file and customize as needed. The file is structured with [section] and [[sub-sections]]. There is a [default] section, followed by additional sections for each available zppy task (climo, ts, e3sm_diags, mpas_analysis, …). Sub-sections can be used to have multiple instances of a particular task, for example regridded monthly or globally averaged time series files. Refer to the zppy documentation for more details.

The key sections of the configuration file are:


  • input, output, www paths may need to be edited.


  • mapping_file path may need to be edited.

  • Typically generate climatology files every 20,50 years: years = begin_year:end_yr:averaging_period – e.g., years = "1:80:20", "1:50:50",


  • mapping_file path may need to be edited.

  • Time series, typically done in chunks of 10 years – e.g., years = "1:80:10"


  • reference_data_path may need to be edited.

  • short_name is a shortened version of the case_name

  • years should match the [climo] section years


Years can be specified separately for time series, climatology and ENSO plots. The lists must have the same lengths and each entry will be mapped to a realization of mpas_analysis:

  • ts_years = "1-50", "1-100",

  • enso_years = "11-50", "11-100",

  • climo_years ="21-50", "51-100",

In this particular example, MPAS Analysis will be run twice. The first realization will produce time series plots covering years 1 to 50, ENSO plots for years 11 to 50 and climatology plots averaged over years 21-50. The second realization will cover years 1-100 for time series, 11-100 for ENSO, 51-100 for climatologies.


  • ts_years should match the [mpas_analysis] section ts_years

  • climo_years should match the [mpas_analysis] section climo_years

See the zppy tutorial for complete configuration file examples.

Launch zppy

Make sure you load the E3SM unified environment.

Run zppy -c post.<case_name>.cfg. This will submit a number of jobs. Run sq to see what jobs are running.

e3sm_diags jobs are dependent on climo and ts jobs, so they wait for those to finish. MPAS Analysis jobs re-use computations, so they are chained. Most jobs run quickly, though MPAS Analysis may take several hours.

These jobs create a new directory <simulations_dir>/<case_name>/post. Each realization will have a shell script (typically bash). This is the actual file that has been submitted to the batch system. There will also be a log file *.o<job ID> as well as a *.status file. The status file indicates the state (WAITING, RUNNING, OK, ERROR). Once all the jobs are complete, you can check their status

If you re-run zppy, it will check status of tasks and will skip any task if its status is “OK”.

As your simulation progresses, you can update the post-processing years in the configuration file and re-run zppy. Newly added task will be submitted, while previously completed ones will be skipped.


If you run ls you’ll probably see files like e3sm_diags_180x360_aave_model_vs_obs_0001-0020.status. This is one e3sm_diags job. Parts of the file name are explained below:


Part of File Name


Part of File Name





Model/obs v. model/obs


First and last years


There is also a corresponding output file. It will have the same name but end with .o<job ID> instead of .status.


The post-processing output is organized hierarchically as follows (where the exact year-ranges are what are defined in the configuration file):

  • <e3sm_simulations_dir>/<case_name>/post/atm/180x360_aave/ts/monthly/10yr has the time series files – one variable per file, in 10 year chunks as defined in <run_scripts_dir>/post.<case_name>.cfg.

  • <e3sm_simulations_dir>/<case_name>/post/atm/180x360_aave/clim/20yr similarly has climatology files for 20 year periods, as defined in <run_scripts_dir>/post.<case_name>.cfg`.

  • <e3sm_simulations_dir>/<case_name>/post/atm/glb/ts/monthly/10yr has globally averaged files for 10 years periods as defined in <run_scripts_dir>/post.<case_name>.cfg.

Documenting the Model Run

You should create a Confluence page for your model run in . Use as a template. See below for how to fill out this template.


code_root_dir and tag_name are defined in <run_scripts_dir>/<case_name>.csh.

The commit hash at the top is the most recent commit.

Add “<branch name>, <commit hash>” to this section of your page.


Compset and Res are specified on in the PACE “Experiment Details” section. See “Performance Information” for how to access PACE. Choose the latest job and list these settings on your page.

Custom parameters should also be listed. Find these by running:

Copy the code blocks after cat <<EOF >> user_nl_eam, cat << EOF >> user_nl_elm, and cat << EOF >> user_nl_mosart to your page.


Push your <run_scripts_dir>/run.<case_name>.csh to , in the archive/v2/beta/coupled directory. Then link it to this section of your page.

Output files

Specify the path to your output files: <simulations_dir>/<case_name>.


Fill out a table with columns for “Job”, “Years”, “Nodes”, “SYPD”, and “Notes”.

Log file names will give you the job IDs. Logs are found in <simulations_dir>/<case_name>/run. If you have done short term archiving, then they will instead be in <simulations_dir>/<case_name>/archive/logs. Use ls to see what logs are in the directory. The job ID will be the two-part (period-separated) number after .log..

PACE’s “Experiment Details” section shows JobID as well. In the table, link each job ID to its corresponding PACE web page. Note that failed jobs will not have a web page on PACE, but you should still list them in the table.

Use zgrep "DATE=" <log> | head -n 1 to find the start date. Use zgrep "DATE=" <log> | tail -n 1 to find the end date. If you would like you can write a bash function to make this easier:

(If zgrep is unavailable, use less <log> to look at a gzipped log file. Scroll down a decent amount to DATE= to find the start date. Use SHIFT+g to go to the end of the file. Scroll up to DATE= to find the end date.)

In the “Years” column specify <start> - <end>, with each in year-month-day format.

To find the number of nodes, first look at the Processor # / Simulation Time chart on PACE. The x-axis lists the highest MPI rank used, with base-0 numbering of ranks. (PE layouts often don’t fit exactly N nodes but instead fill N-1 nodes and have some number of ranks left over on the final node, leaving some cores on that node unused.) Then find MPI tasks/node in the “Experiment Details” section. The number of nodes can then be calculated as ceil((highest MPI rank + 1)/ (MPI tasks/node)).

The SYPD (simulated years per day) is listed in PACE’s “Experiment Details” section as Model Throughput.

In the “Notes” section, mention if a job failed or if you changed anything before re-running a job.

Global time series

Be sure to have set the [global_time_series] task in zppy.

Example configuration:

That will produce <figstr>.pdf and <figstr>.png. They will be available automatically at <www>/<case_name>/<figstr>.png. You can download the image from the website and then upload it to your Confluence page.

E3SM Diags

The template page already includes baseline diagnostics. Add your own diagnostics links labeled as <start_year>-<end_year>.

Your diagnostics are located at the web address corresponding to the www path in <run_scripts_dir>/<case_name>.cfg.

See for finding the URLs for the web portals on each E3SM machine (listed as <web_address>).

Fill the table with the specific web links: e.g.,<username>/E3SM/v2/beta/<case_name>/e3sm_diags/180x360_aave/model_vs_obs_0001-0020/viewer/.

MPAS Analysis

See for finding the URLs for the web portals on each E3SM machine (listed as <web_address>)

Make a bulleted list of links, e.g., for<username>/E3SM/v2/beta/<case_name>/mpas_analysis/ts_0001-0050_climo_0021-0050/, create a bullet “1-50 (time series), 21-50 (climatology)”.

Long Term Archiving with zstash

Simulations that are deemed sufficiently valuable should be archived using zstash for long-term preservation.

You can ask questions about zstash on

Compy, Anvil and Chrysalis do not have local HPSS. We rely on NERSC HPSS for long-term archiving.

If you are archiving a simulation run on Compy or LCRC (Chrysalis/Anvil), do all of the following steps. If you are archiving a simulation run on NERSC (Cori), skip to step 4.

1. Clean up directory

Log into the machine that you ran the simulation on.

Remove all eam.i files except the latest one. Dates are of the form <YYYY-MM-DD>.

There may still be more files than is necessary to archive. You can probably remove *.err, *.lock, *debug_block*, *ocean_block_stats* files.


2. zstash create & Transfer to NERSC HPSS

2.a. E3SM Unified v1.6.0 / zstash v1.2.0 or greater

If you are using E3SM Unified v1.6.0 or greater, has enabled Globus ( ) transfer with zstash create.

On the machine that you ran the simulation on:

If you don’t have one already, create a directory for utilities, e.g., utils. Then open a file in that directory called batch_zstash_create.bash and paste the following in it, making relevant edits:

Commands to load the E3SM Unified environment for each machine can be found at .

Then, do the following:

Then, on NERSC/Cori:

2.b. Earlier releases

2.b.i. zstash create

On the machine that you ran the simulation on:

If you don’t have one already, create a directory for utilities, e.g., utils. Then open a file in that directory called batch_zstash_create.bash and paste the following in it, making relevant edits:

Commands to load the E3SM Unified environment for each machine can be found at .

Then, do the following:

2.b.ii. Transfer to NERSC

On a NERSC machine (Cori):

Log into Globus, using your NERSC credentials:

  1. (Left hand side): Transfer from <the machine's DTN> <simulations_dir>/<case_name>/zstash

  2. Click enter on path and "select all" on left-hand side

  3. Transfer to NERSC DTN /global/cfs/cdirs/e3sm/<username>/E3SMv2/<case_name>

    1. Notice we're using cfs rather than scratch on Cori

  4. Click enter on the path

  5. Click “Transfer & Sync Options” in the center.

  6. Choose:

    1. “sync - only transfer new or changed files” (choose “modification time is newer” in the dropdown box)

    2. “preserve source file modification times”

    3. “verify file integrity after transfer”

  7. For “Label This Transfer”: “zstash <case_name> <machine name> to NERSC”

  8. Click "Start" on the left hand side.

You should get an email from Globus when the transfer is completed. (On Chrysalis, for 165 years of data, this transfer takes ~13 hours).

2.b.iii. Transfer to HPSS

On a NERSC machine (Cori):

3. zstash check

On a NERSC machine (Cori):

Paste the following in that file, making relevant edits:

Commands to load the E3SM Unified environment for each machine can be found at .

If you’re using E3SM Unified v1.6.0 / zstash v1.2.0 (or greater) and you want to check a long simulation, you can use the --tars option introduced in to split the checking into more manageable pieces:

# Starting at 00005a until the end zstash check --tars=00005a- # Starting from the beginning to 00005a (included) zstash check --tars=-00005a # Specific range zstash check --tars=00005a-00005c # Selected tar files zstash check --tars=00003e,00004e,000059 # Mix and match zstash check --tars=000030-00003e,00004e,00005a-

Then, do the following:

4. Document

On a NERSC machine (Cori):

Update simulation Confluence page with information regarding this simulation (For Water Cycle’s v2 work, that page is ) . In the zstash archive column, specify:

  • /home/<first letter>/<username>/E3SMv2/<case_name>

  • zstash_create_<stamp>.log

  • zstash_check_<stamp>.log

5. Delete files

On a NERSC machine (Cori):

On the machine that you ran the simulation on:

More info

Refer to zstash's best practices for E3SM for details.

Publishing the simulation data (Optional)

E3SM Project has policy to publish all official simulation campaigns once those simulations are documented in publications. Refer to step 3 in for guidance on requesting data publication.