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Merge pull request #4595 from ESMCI/mkstratos/nbfb-test-update
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Points the TSC and PGN tests to updated input data for E3SMv3

Test suite: e3sm_atm_nbfb

User interface changes?: N

Update gh-pages html (Y/N)?: N
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@rljacob
rljacob authored Mar 20, 2024
2 parents 58d9eb0 + 5115e0d commit 090fa26
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9 changes: 4 additions & 5 deletions CIME/SystemTests/pgn.py
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Expand Up @@ -46,7 +46,7 @@
)
FCLD_NC = "cam.h0.cloud.nc"
INIT_COND_FILE_TEMPLATE = (
"20231105.v3b01.F2010.ne4_oQU240.chrysalis.{}.{}.0002-{:02d}-01-00000.nc"
"20240305.v3p0p0.F2010.ne4pg2_oQU480.chrysalis.{}.{}.0002-{:02d}-01-00000.nc"
)
INSTANCE_FILE_TEMPLATE = "{}{}_{:04d}.h0.0001-01-01-00000{}.nc"

Expand Down Expand Up @@ -97,8 +97,8 @@ def build_phase(self, sharedlib_only=False, model_only=False):
logger.debug("PGN_INFO: Updating user_nl_* files")

csmdata_root = self._case.get_value("DIN_LOC_ROOT")
csmdata_atm = os.path.join(csmdata_root, "atm/cam/inic/homme/ne4_v3_init")
csmdata_lnd = os.path.join(csmdata_root, "lnd/clm2/initdata/ne4_oQU240_v3_init")
csmdata_atm = os.path.join(csmdata_root, "atm/cam/inic/homme/ne4pg2_v3_init")
csmdata_lnd = os.path.join(csmdata_root, "lnd/clm2/initdata/ne4pg2_v3_init")

iinst = 1
for icond in range(1, NUMBER_INITIAL_CONDITIONS + 1):
Expand Down Expand Up @@ -236,11 +236,10 @@ def _compare_baseline(self):
viewing = (
"{}\n"
" EVV viewing instructions can be found at: "
" https://github.com/E3SM-Project/E3SM/blob/master/cime/scripts/"
" https://github.com/ESMCI/CIME/blob/master/scripts/"
"climate_reproducibility/README.md#test-passfail-and-extended-output"
"".format(evv_out_dir)
)

comments = (
"{} {} for test '{}'.\n"
" {}\n"
Expand Down
8 changes: 4 additions & 4 deletions CIME/SystemTests/tsc.py
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Expand Up @@ -33,7 +33,7 @@
OUT_FREQ = 10 # seconds
INSPECT_AT = [300, 450, 600] # seconds
INIT_COND_FILE_TEMPLATE = (
"20231105.v3b01.F2010.ne4_oQU240.chrysalis.{}.{}.0002-{:02d}-01-00000.nc"
"20240305.v3p0p0.F2010.ne4pg2_oQU480.chrysalis.{}.{}.0002-{:02d}-01-00000.nc"
)
VAR_LIST = [
"T",
Expand Down Expand Up @@ -102,8 +102,8 @@ def _run_with_specified_dtime(self, dtime=2):
self._case.set_value("STOP_OPTION", "nsteps")

csmdata_root = self._case.get_value("DIN_LOC_ROOT")
csmdata_atm = os.path.join(csmdata_root, "atm/cam/inic/homme/ne4_v3_init")
csmdata_lnd = os.path.join(csmdata_root, "lnd/clm2/initdata/ne4_oQU240_v3_init")
csmdata_atm = os.path.join(csmdata_root, "atm/cam/inic/homme/ne4pg2_v3_init")
csmdata_lnd = os.path.join(csmdata_root, "lnd/clm2/initdata/ne4pg2_v3_init")

nstep_output = OUT_FREQ // dtime
for iinst in range(1, NINST + 1):
Expand Down Expand Up @@ -225,7 +225,7 @@ def _compare_baseline(self):
viewing = (
"{}\n"
" EVV viewing instructions can be found at: "
" https://github.com/E3SM-Project/E3SM/blob/master/cime/scripts/"
" https://github.com/ESMCI/CIME/blob/master/scripts/"
"climate_reproducibility/README.md#test-passfail-and-extended-output"
"".format(evv_out_dir)
)
Expand Down
84 changes: 42 additions & 42 deletions scripts/climate_reproducibility/README.md
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Expand Up @@ -51,64 +51,64 @@ Primarily, the statistical analysis of the climates is done through [EVV](https:
which will generate a portable test website to describe the results (pass or fail) in detail (see the extended output
section below).

For E3SM supported machines, the `e3sm_simple` conda environment is provided for these tests and includes the `EVV`
conda package. You can activate the `e3sm_simple` environment in the same way as `e3sm_unified` environment:
For E3SM supported machines, the `cime_env` conda environment is provided for these tests and includes the `EVV`
conda package. You can activate the `cime_env` environment in the same way as `e3sm_unified` environment:

```
source <activate_path>/load_latest_e3sm_simple.sh
source <activate_path>/load_latest_cime_env.sh
```

where `<activate_path>` is the machine-specific location of the activation script as described on this confluence page:

https://acme-climate.atlassian.net/wiki/spaces/EIDMG/pages/780271950/Diagnostics+and+Analysis+Quickstart#DiagnosticsandAnalysisQuickstart-Accessingmetapackagesoftwarebyactivatingacondaenvironment

If you don't have access to confluence or are unable to activate this environment for whatever reason, you can install
your own `e3sm_simple` conda environment with this command (once you have anaconda/miniconda installed):
your own `cime_env` conda environment with this command (once you have anaconda/miniconda installed):

```
conda create -n e3sm-simple -c conda-forge -c e3sm e3sm-simple
conda create -n cime-env -c conda-forge -c e3sm cime-env
```

*NOTE: If you run into problems with getting this environment working on your machine, please open an issue on E3SM's
Github and tag @jhkennedy, or send Joseph H. Kennedy <kennedyjh@ornl.gov> an email.*
Github and tag @mkstratos.

After you've activated the `e3sm_simple` environment, change to the `$E3SM/cime/scripts` directory (where `$E3SM` is the
After you've activated the `cime_env` environment, change to the `$E3SM/cime/scripts` directory (where `$E3SM` is the
directory containing E3SM). Then to run one of the tests, you will use the `create_test` script like normal.
To run the `MVK` test and generate a baseline, you would run a command like:

```
./create_test MVK_PL.ne4_oQU240.FC5AV1C-L -g --baseline-root "/PATH/TO/BASELINE"
./create_test MVK_PS.ne4pg2_oQU480.F2010 -g --baseline-root "/PATH/TO/BASELINE"
```

And to compare to the baseline, you would run a command like:

```
./create_test MVK_PL.ne4_oQU240.FC5AV1C-L -c --baseline-root "/PATH/TO/BASELINE"
./create_test MVK_PS.ne4pg2_oQU480.F2010 -c --baseline-root "/PATH/TO/BASELINE"
```

*NOTE: The MVK run a 20 member ensemble for at least 13 months (using the last 12 for the
*NOTE: The MVK runs a 30 member ensemble for 13 months (using the last 12 for the
statistical tests) and, depending on the machine, may take some fiddling to execute within a particular
queue's wallclock time limit. You may want to over-ride the requested walltime using `--walltime HH:MM:SS`
option to `create_test`.*

The full set of commands to run the MVK test used on Cori are:
The full set of commands to run the MVK test used on Perlmutter are:

*Generate a baseline*
```
cd $E3SM/cime/scripts
source /global/project/projectdirs/acme/software/anaconda_envs/load_latest_e3sm_simple.sh
source /global/common/software/e3sm/anaconda_envs/load_latest_cime_env.sh
./create_test MVK_PL.ne4_ne4.FC5AV1C-L --baseline-root "${CSCRATCH}/baselines" --project acme -g -o --walltime 01:00:00
./create_test MVK_PS.ne4pg2_oQU480.F2010 --baseline-root "${PSCRATCH}/baselines" --project e3sm -g -o --walltime 01:00:00
```

*Compare to a baseline*
```
cd $E3SM/cime/scripts
source /global/project/projectdirs/acme/software/anaconda_envs/load_latest_e3sm_simple.sh
source /global/common/software/e3sm/anaconda_envs/load_latest_cime_env.sh
./create_test MVK_PL.ne4_ne4.FC5AV1C-L --baseline-root "${CSCRATCH}/baselines" --project acme -c --walltime 01:00:00
./create_test MVK_PS.ne4pg2_oQU480.F2010 --baseline-root "${PSCRATCH}/baselines" --project e3sm -c --walltime 01:00:00
```

## Test pass/fail and extended output
Expand All @@ -117,9 +117,9 @@ When you launch these tests and compare to a baseline, CIME will output the loca
something like this:

```
# On cori-knl:
./create_test MVK_PL.ne4_ne4.FC5AV1C-L --baseline-root "${CSCRATCH}/baselines" --project acme -c --walltime 01:00:00
Creating test directory /global/cscratch1/sd/${USER}/acme_scratch/cori-knl/MVK_PL.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.YYYYMMDD_HHMMSS_RANDOMID
# On pm-cpu:
./create_test MVK_PS.ne4pg2_oQU480.F2010 --baseline-root "${PSCRATCH}/baselines" --project e3sm -c --walltime 01:00:00
Creating test directory ${PSCRATCH}/e3sm_scratch/pm-cpu/MVK_PS.ne4pg2_oQU480.F2010.pm-cpu_intel.C.YYYYMMDD_HHMMSS_RANDOMID
```

Let's call that directory `$CASE_DIR`. Once all the jobs are finished, navigate to that directory and
Expand All @@ -129,7 +129,7 @@ you can `cat TestStatus` to determine if the test passed or failed by looking at
cd $CASE_DIR
cat TestStatus
...
PASS MVK_PL.ne4_ne4.FC5AV1C-L.cori-knl_intel BASELINE
PASS MVK_PS.ne4pg2_oQU480.F2010.pm-cpu_intel BASELINE
...
```
Expand All @@ -139,8 +139,8 @@ To get some basic summary statistics about the test that was run, look in the `T
```
2019-08-14 22:09:02: BASELINE PASS for test 'YYYYMMDD_HHMMSS_RANDOMID'.
Case: YYYYMMDD_HHMMSS_RANDOMID; Test status: pass; Variables analyzed: 118; Rejecting: 0; Critical value: 13; Ensembles: statistically identical
EVV results can be viewed at: /global/cscratch1/sd/${USER}/acme_scratch/cori-knl/MVK_PL.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.YYYYMMDD_HHMMSS_RANDOMID/run/MVK_PL.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.YYYYMMDD_HHMMSS_RANDOMID.evv/
EVV viewing instructions can be found at: https://github.com/E3SM-Project/E3SM/blob/master/cime/scripts/climate_reproducibility/README.md#test-passfail-and-extended-output
EVV results can be viewed at: ${PSCRATCH}/e3sm_scratch/pm-cpu/MVK_PS.ne4pg2_oQU480.F2010.pm-cpu_intel.C.YYYYMMDD_HHMMSS_RANDOMID/run/MVK_PS.ne4pg2_oQU480.F2010.pm-cpu_intel.C.YYYYMMDD_HHMMSS_RANDOMID.evv/
EVV viewing instructions can be found at: https://github.com/ESMCI/CIME/blob/master/scripts/climate_reproducibility/README.md#test-passfail-and-extended-output
```

EVV reports the location of the output website where you can see the details of the analysis. For
Expand All @@ -153,18 +153,18 @@ the website directory to your machine and view it using EVV.

### View via ssh

For this example, we'll assume the tests were run on Cori at NERSC, but these instructions should be
easily adaptable to any E3SM supported machine. First, log into Cori via ssh and connect your local
8080 port to the 8080 port on Cori:
For this example, we'll assume the tests were run on Perlmutter at NERSC, but these instructions should be
easily adaptable to any E3SM supported machine. First, log into Perlmutter via ssh and connect your local
8080 port to the 8080 port on Perlmutter:

```
ssh -L 8080:localhost:8080 [USER]@cori.nersc.gov
ssh -L 8080:localhost:8080 [USER]@saul-p1.nersc.gov
```

Activate the `e3sm_simple` environment:
Activate the `cime_env` environment:

```
source /global/project/projectdirs/acme/software/anaconda_envs/load_latest_e3sm_simple.sh
source /global/common/software/e3sm/anaconda_envs/load_latest_cime_env.sh
```

Navigate to the case's run directory:
Expand All @@ -176,7 +176,7 @@ pushd ${CASE_DIR}/run
Then, using EVV, serve the website over port 8080:

```
evv -o PGN_P1x1.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.YYYYMMDD_HHMMSS_RANDOMID.evv -s 8080
evv -o PGN_P1x1.ne4pg2_oQU480.F2010.pm-cpu_intel.C.YYYYMMDD_HHMMSS_RANDOMID.evv -s 8080
```

Evv will then report to you the URL where you can view the website:
Expand All @@ -194,17 +194,17 @@ Evv will then report to you the URL where you can view the website:
Extended Verification and Validation for Earth System Models
--------------------------------------------------------------------
Current run: 2019-08-27 14:16:49
User: kennedyj
OS Type: Linux 4.12.14-150.27-default
Machine: cori07
Current run: 2024-03-06 07:56:37
User: mek
OS Type: Linux 5.14.21-150400.24.81_12.0.87-cray_shasta_c
Machine: login31
Serving HTTP on 0.0.0.0 port 8080 (http://0.0.0.0:8080/)
View the generated website by navigating to:
http://0.0.0.0:8080/PGN_P1x1.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.YYYYMMDD_HHMMSS_RANDOMID.evv/index.html
http://0.0.0.0:8080/PGN_P1x1.ne4pg2_oQU480.F2010.pm-cpu_intel.C.YYYYMMDD_HHMMSS_RANDOMID.evv/index.html
Exit by pressing `ctrl+c` to send a keyboard interrupt.
```
Expand All @@ -214,20 +214,20 @@ browser to view the output website.

### View a local copy

For this example, we'll assume the tests were run on Cori at NERSC, but these instructions should be
easily adaptable to any E3SM supported machine. Install `e3sm_simple` locally and activate it:
For this example, we'll assume the tests were run on Perlmutter at NERSC, but these instructions should be
easily adaptable to any E3SM supported machine. Install `cime_env` locally and activate it:

```
conda create -n e3sm_simple -c conda-forge -c e3sm e3sm-simple
conda activate e3sm_simple
conda create -n cime_env -c conda-forge -c e3sm cime-env
conda activate cime_env
```

Then, copy the website to your local machine, and view it:

```
# on your local machine
scp -r /global/cscratch1/sd/${USER}/acme_scratch/cori-knl/MVK_PL.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.YYYYMMDD_HHMMSS_RANDOMID/run/MVK_PL.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.YYYYMMDD_HHMMSS_RANDOMID.evv .
evv -o MVK_PL.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.YYYYMMDD_HHMMSS_RANDOMID.evv -s
scp -r ${PSCRATCH}/e3sm_scratch/pm-cpu/MVK_PS.ne4pg2_oQU480.F2010.pm-cpu_intel.C.YYYYMMDD_HHMMSS_RANDOMID/run/MVK_PS.ne4pg2_oQU480.F2010.pm-cpu_intel.C.YYYYMMDD_HHMMSS_RANDOMID.evv .
evv -o MVK_PS.ne4pg2_oQU480.F2010.pm-cpu_intel.C.YYYYMMDD_HHMMSS_RANDOMID.evv -s
--------------------------------------------------------------------
______ __ __ __ __
| ____| \ \ / / \ \ / /
Expand All @@ -249,7 +249,7 @@ evv -o MVK_PL.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.YYYYMMDD_HHMMSS_RANDOMID.evv -s
View the generated website by navigating to:
http://0.0.0.0:8000/MVK_PL.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.YYYYMMDD_HHMMSS_RANDOMID.evv/index.html
http://0.0.0.0:8000/MVK_PS.ne4pg2_oQU480.F2010.pm-cpu_intel.C.YYYYMMDD_HHMMSS_RANDOMID.evv/index.html
Exit by pressing `ctrl+c` to send a keyboard interrupt.
Expand All @@ -262,6 +262,6 @@ browser to view the output website.
**Please note:** the output website uses some JavaScript to render elements of the page (especially figures),
and opening up the `index.html` file using the `file://` protocol in a web browser will likely not work
well (most browser have stopped allowing access to "local resources" like JavaScript through the `file://`
protocol). You can view the website by either copying it to a hosted location (`~/WWW` which is hosted at
`http://users.nccs.gov/~user` on Titan, for example) or copying it to your local machine and running a
protocol). You can view the website by either copying it to a hosted location (`/global/cfs/projectdirs/e3sm/www/${USER}` which is hosted at
`https://portal.nersc.gov/project/e3sm/${USER}` on NERSC, for example) or copying it to your local machine and running a
local http server (included in python!) and viewing it through an address like `http://0.0.0.0:8000/index.html`.

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