From b9efcb17a18d5fd6a592cd9913c40b6a750e346f Mon Sep 17 00:00:00 2001 From: jvgeiger Date: Mon, 17 Jul 2023 19:02:07 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20NASA-LIS?= =?UTF-8?q?/LISF@8151304056f2a8e5a7386d631e5361c265cac16e=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- LDT_users_guide/LDT_users_guide.html | 6 +- .../LISF_installation_guide.html | 2 +- LIS_users_guide/LIS_users_guide.html | 2 +- LVT_users_guide/LVT_users_guide.html | 2 +- .../creating_a_custom_modulefile.html | 2 +- .../discover_quick_start.html | 2 +- .../howto_create_lis_testcases.html | 2 +- index.html | 2 +- .../public_testcase_walkthrough.html | 188 +++++++++++++----- working_with_github/working_with_github.html | 2 +- 10 files changed, 150 insertions(+), 60 deletions(-) diff --git a/LDT_users_guide/LDT_users_guide.html b/LDT_users_guide/LDT_users_guide.html index f11889e94..bd6bdefe1 100644 --- a/LDT_users_guide/LDT_users_guide.html +++ b/LDT_users_guide/LDT_users_guide.html @@ -2925,7 +2925,7 @@

7.3. Parameters

MODIS_Native

-

Terra-MODIS sensor-based IGBP land classification map, modified by NCEP. For more info, please see: http://www.ral.ucar.edu/research/land/technology/noahmp_lsm.php

+

Terra-MODIS sensor-based IGBP land classification map, modified by NCEP. For more info, please see: https://ral.ucar.edu/model/noah-multiparameterization-land-surface-model-noah-mp-lsm

MODIS_LIS

@@ -2937,7 +2937,7 @@

7.3. Parameters

USGS_Native

-

The 24-category USGS native landcover map. See: http://www.ral.ucar.edu/research/land/technology/noahmp_lsm.php

+

The 24-category USGS native landcover map. See: https://ral.ucar.edu/model/noah-multiparameterization-land-surface-model-noah-mp-lsm

USGS_LIS

@@ -17757,7 +17757,7 @@

References

diff --git a/howto_create_lis_testcases/howto_create_lis_testcases.html b/howto_create_lis_testcases/howto_create_lis_testcases.html index 51df77d6c..c80fa1fd9 100644 --- a/howto_create_lis_testcases/howto_create_lis_testcases.html +++ b/howto_create_lis_testcases/howto_create_lis_testcases.html @@ -839,7 +839,7 @@

Finishing Up

diff --git a/index.html b/index.html index 64fa0281b..110667fe4 100644 --- a/index.html +++ b/index.html @@ -668,7 +668,7 @@

emacs

diff --git a/public_testcase_walkthrough/public_testcase_walkthrough.html b/public_testcase_walkthrough/public_testcase_walkthrough.html index 2d9ee5dfb..839d41a47 100644 --- a/public_testcase_walkthrough/public_testcase_walkthrough.html +++ b/public_testcase_walkthrough/public_testcase_walkthrough.html @@ -438,8 +438,8 @@ @@ -527,7 +527,7 @@

Clone the LISF Repository

-
% git clone -b support/lisf-public-7.3 git@github.com:NASA-LIS/LISF.git
+
% git clone -b support/lisf-public-7.4 github:NASA-LIS/LISF.git
 % cd LISF
@@ -538,7 +538,7 @@

Clone the LISF Repository

-The support/lisf-public-7.3 branch is known to be compatible with the testcase files. The master branch may contain changes to the LISF source code that break compatibility with the testcase files. We therefore recommend using the support branch while working through these testcases. +The support/lisf-public-7.4 branch is known to be compatible with the testcase files. The master branch may contain changes to the LISF source code that break compatibility with the testcase files. We therefore recommend using the support branch while working through these testcases. @@ -549,11 +549,23 @@

Configure and Compile the LI

For information about configuration settings and detailed compilation instructions, see the LISF Users' Guides. In general, the compilation process for each component is as follows:

+
+ + + + + +
+ + +As you run these testcases, you will have the opportunity to compare your output to TARGET_OUTPUT files or "solutions". The TARGET_OUTPUT files were created by running ldt, lis, and lvt compiled with default compile configuration settings. For this walkthrough, it is recommended that you also use default compiler configuration settings. +
+
% cd ldt
 % ./configure
-> # Select compile configuration settings (see Docs)...
+> # Select compile configuration settings (Default settings recommended.)
 % ./compile
 > # Compilation output...
 % mv LDT ../../            # move executable up into $WORKING_DIR
@@ -566,6 +578,9 @@ 
Configure and Compile the LI
 

 
Change directories back into your $WORKING_DIR which should now contain three executable files: LDT, LIS, LVT.

 

+

+
If you ever wish to generate new executable files, cd into /LISF/l??/make and run gmake realclean.  This will clear all dependency files and allow you to cleanly define new compile configuration settings and recompile.

+
@@ -618,7 +633,7 @@

Download Input and Target Files

-The tar file for this step is approximately 350MB compressed and 4.1GB unpacked. Ensure that you have enough storage available before downloading testcase files. +The tar file for this step is approximately 350MB compressed and 4.2GB unpacked. Ensure that you have enough storage available before downloading testcase files. @@ -628,8 +643,8 @@

Download Input and Target Files

-
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase1_ldt_parms_2020.tar.gz
-% tar -xzf testcase1_ldt_parms_2020.tar.gz -C .
+
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase1_ldt_parms_2023.tar.gz
+% tar -xzf testcase1_ldt_parms_2023.tar.gz -C .
@@ -738,7 +753,7 @@

The LDT Configuration File

-

LISF configuration files use relative paths to describe file locations. Keep this in mind if you encounter any file not found errors.

+

LISF configuration files use relative paths to describe file locations. Keep this in mind if you encounter any "file not found" errors.

@@ -826,7 +841,19 @@

Run LDT - The Parameter Processi

-

The run should take a few minutes to complete. If the run aborts, troubleshoot the issue by reviewing any errors printed to the terminal and by viewing the contents of ldtlog.0000. If no errors print to the terminal, verify that the run completed successfully by checking for the following confirmation at the end of the ldtlog.0000:

+

The run should take a few minutes to complete. If the run aborts, troubleshoot the issue by reviewing any errors printed to the terminal and by viewing the contents of ldtlog.0000. If no errors print to the terminal, verify that the run completed successfully by checking for the following confirmation at the end of the ldtlog.0000.

+
+
+ + + + + +
+ + +If the terminal reports the error "./LDT: symbol lookup error:", this may be due extraneous modules loaded into your environement that do not allow lis to run properly. View your modules using the command module list. If extraneous modules are loaded, run module purge to clear your environment and then module load [lisf module file] to load an environment suitable to running LISF. See the "discover_quick_start" document in the LISF Users' Guides for more information. +
@@ -837,6 +864,32 @@

Run LDT - The Parameter Processi --------------------------------

+
+ + + + + +
+ + +
+

ldt, lis, and lvt can also be run by submitting batch jobs using SLURM (Simple Linux Utility for Resource Management). If you are running this tutorial on Discover, you can download example batch scripts for all steps from the LIS Testcase website using the following command:

+
+
+
+
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase_batch_scripts.tar.gz
+% tar -xzf testcase_batch_scripts.tar.gz -C .
+
+
+
+

The batch scripts (step*.job) will unpack into the appropriate directories. To submit a job to discover using a batch script, use the command sbatch [BATCH SCRIPT] from the same directory as the job you wish to run. The command squeue -u [YOUR USER ID] will provide updates on your job. If the job crashes, troubleshoot using any slurm.out files.

+
+
+

See the NCCS Discover Jobs Users' Guide for more information.

+
+
+

LDT Output Files

@@ -855,11 +908,11 @@

LDT Output Files

ldtlog.0000

-

The runtime configuration file read by LDT in this stepThe output diagnostic file that provides runtime messages, including warnings and error messages. This file is useful for verifying successful run completion and troubleshooting unsuccessful runs.

+

The output diagnostic file that provides runtime messages, including warnings and error messages. This file is useful for verifying successful run completion and troubleshooting unsuccessful runs.

MaskParamFill.log

-

The "target" NetCDF file generated by LDT in this step. This diagnostic file informs of any disagreements between an LSM-based parameter and the landmask, and whether any parameter gridcells were "filled" to agree with the landmask.

+

This diagnostic file informs of any disagreements between an LSM-based parameter and the landmask, and whether any parameter gridcells were "filled" to agree with the landmask.

@@ -878,7 +931,7 @@

LDT Output Files

The LIS Parameter File

-

The contents of the LIS parameter input file produced by LDT can be examined visually using a command-line program such as ncview or a desktop application like NASA’s Panoply. For this walkthrough we will be using ncview.

+

The contents of the LIS parameter input file produced by LDT can be examined visually using a command-line program such as ncview or a desktop application like NASA’s Panoply. For this walkthrough we will be using ncview. If needed, add ncview to your environment by running, module load ncview.

Open the LIS input file using ncview:

@@ -1042,7 +1095,7 @@

Compare the Output

-The nccmp command will be used in future steps. Going forward, some files may not be identical, but any differences reported should be small. +The nccmp command will be used in future steps. Going forward, some files may not be identical, but any differences reported should be small. Also note: in this step, the target lis input file was generated using Soil texture spatial transform: mode @@ -1094,7 +1147,7 @@

Download Input and Target Files

-The tar file for this step is approximately 67MB compressed and 250MB unpacked. Ensure that you have enough storage available before downloading testcase files. +The tar file for this step is approximately 65MB compressed and 343MB unpacked. Ensure that you have enough storage available before downloading testcase files. @@ -1104,8 +1157,8 @@

Download Input and Target Files

-
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase2_lis_ol_2020.tar.gz
-% tar -xzf testcase2_lis_ol_2020.tar.gz -C .
+
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase2_lis_ol_2023.tar.gz
+% tar -xzf testcase2_lis_ol_2023.tar.gz -C .
@@ -1191,13 +1244,13 @@

Download the Meteorologica
  1. -

    If needed, install wget.

    +

    If needed, install wget

  2. -

    Create a NASA Earthdata account if you do not already have one.

    +

    Create a NASA Earthdata account if you do not already have one

  3. -

    Follow steps 1-4 in these instructions to save your NASA Earthdata login credentials locally.

    +

    Follow steps 1-3 in these instructions to save your NASA Earthdata login credentials locally

@@ -1280,7 +1333,7 @@

Run LIS - The "Open-Loop" (OL) Step

-

With a single processor the run should take approximately 20 minutes to complete. If the run fails, diagnose the issue by reviewing any errors that have printed to the terminal and by viewing the contents of lislog files (if any are present). If no errors appear and the run appears to have completed successfully, examine the end of any lislog files present to check for a confirmation message:

+

With a single processor the run should take approximately 20 minutes to complete. If the run fails, diagnose the issue by reviewing any errors that have printed to the terminal and by viewing the contents of lislog files (located in the log directory as defined by line 42 of lis.config_noah36_ol). If no errors appear and the run appears to have completed successfully, examine the end of any lislog files present to check for a confirmation message:

@@ -1385,7 +1438,7 @@

Download Input and Target Files

-The tar file for this step is approximately 77KB compressed and 180KB unpacked. Ensure that you have enough storage available before downloading testcase files. +The tar file for this step is approximately 97KB compressed and 100KB unpacked. Ensure that you have enough storage available before downloading testcase files. @@ -1395,8 +1448,8 @@

Download Input and Target Files

-
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase3_ldt_ensrst_2020.tar.gz
-% tar -xzf testcase3_ldt_ensrst_2020.tar.gz -C .
+
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase3_ldt_ensrst_2023.tar.gz
+% tar -xzf testcase3_ldt_ensrst_2023.tar.gz -C .
@@ -1495,7 +1548,19 @@

Run LDT - Generate Ensemble Re

-

The run should take a few minutes to complete. If the run aborts, troubleshoot the issue by reviewing any errors printed to the terminal and by viewing the contents of ldtlog.0000. If no errors print to the terminal, verify that the run completed successfully by checking for the following confirmation at the end of the ldtlog.0000:

+

The run should take a few minutes to complete. If the run aborts, troubleshoot the issue by reviewing any errors printed to the terminal and by viewing the contents of ldtlog.0000. If no errors print to the terminal, verify that the run completed successfully by checking for the following confirmation at the end of the ldtlog.0000.

+
+
+ + + + + +
+ + +If the terminal reports the error "./LDT: symbol lookup error:", this may be due extraneous modules loaded into your environement that do not allow lis to run properly. View your modules using the command module list. If extraneous modules are loaded, run module purge to clear your environment and then module load [lisf module file] to load an environment suitable to running LISF. See the "discover_quick_start" document in the LISF Users' Guides for more information. +
@@ -1513,7 +1578,7 @@

LDT Output Files

During this run, LDT produced one output file named LIS_EnRST_NOAH36_201801010000.d01.nc and placed it into the $WORKING_DIR/DA_ensrst directory.

-

Use ncview, Panoply, Matlab or any other viewing package that supports NetCDF files. Compare what you see with the target version of this output file, also located in $WORKING_DIR/D_ensrst. Additionally, you can use nccmp to directly compare the contents of the file created by your LDT run and the target.

+

Use ncview, Panoply, Matlab or any other viewing package that supports NetCDF files. Compare what you see with the target version of this output file, also located in $WORKING_DIR/DA_ensrst. Additionally, you can use nccmp to directly compare the contents of the file created by your LDT run and the target. If there are differences between your file and the target file, you can use ncdiff to create a new NetCDF file to visualize the differences.

@@ -1568,7 +1633,7 @@

Download Input and Target Files

-The tar file for this step is approximately 362KB compressed and 815KB unpacked. Ensure that you have enough storage available before downloading testcase files. +The tar file for this step is approximately 384KB compressed and 803KB unpacked. Ensure that you have enough storage available before downloading testcase files. @@ -1578,8 +1643,8 @@

Download Input and Target Files

-
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase4_ldt_lsmcdf_2020.tar.gz
-% tar -xzf testcase4_ldt_lsmcdf_2020.tar.gz -C .
+
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase4_ldt_lsmcdf_2023.tar.gz
+% tar -xzf testcase4_ldt_lsmcdf_2023.tar.gz -C .
@@ -1696,7 +1761,19 @@

Run LDT - DA Preprocessing Step

-

The run should take a few minutes to complete. If the run aborts, troubleshoot the issue by reviewing any errors printed to the terminal and by viewing the contents of ldtlog.0000. If no errors print to the terminal, verify that the run completed successfully by checking for the following confirmation at the end of the ldtlog.0000:

+

The run should take a few minutes to complete. If the run aborts, troubleshoot the issue by reviewing any errors printed to the terminal and by viewing the contents of ldtlog.0000. If no errors print to the terminal, verify that the run completed successfully by checking for the following confirmation at the end of the ldtlog.0000.

+
+
+ + + + + +
+ + +If the terminal reports the error "./LDT: symbol lookup error:", this may be due extraneous modules loaded into your environement that do not allow lis to run properly. View your modules using the command module list. If extraneous modules are loaded, run module purge to clear your environment and then module load [lisf module file] to load an environment suitable to running LISF. See the "discover_quick_start" document in the LISF Users' Guides for more information. +
@@ -1744,7 +1821,7 @@

Download Input and Target Files

-The tar file for this step is approximately 4.5GB compressed and 5.3GB unpacked. Ensure that you have enough storage available before downloading testcase files. +The tar file for this step is approximately 4.6GB compressed and 9.1GB unpacked. Ensure that you have enough storage available before downloading testcase files. @@ -1754,8 +1831,8 @@

Download Input and Target Files

-
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase5_ldt_obscdf_2020.tar.gz
-% tar -xzf testcase5_ldt_obscdf_2020.tar.gz -C .
+
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase5_ldt_obscdf_2023.tar.gz
+% tar -xzf testcase5_ldt_obscdf_2023.tar.gz -C .
@@ -1884,7 +1961,7 @@

The LDT Configuration File

4 -Averaging interval used while computing CDF. In this case, one day. +Averaging interval used while computing the CDF. In this case, one day. 5 @@ -1929,7 +2006,19 @@

Run LDT - DA Preprocessing Step

-

The run should take a few minutes to complete. If the run aborts, troubleshoot the issue by reviewing any errors printed to the terminal and by viewing the contents of ldtlog.0000. If no errors print to the terminal, verify that the run completed successfully by checking for the following confirmation at the end of the ldtlog.0000:

+

The run should take a few minutes to complete. If the run aborts, troubleshoot the issue by reviewing any errors printed to the terminal and by viewing the contents of ldtlog.0000. If no errors print to the terminal, verify that the run completed successfully by checking for the following confirmation at the end of the ldtlog.0000.

+
+
+ + + + + +
+ + +If the terminal reports the error "./LDT: symbol lookup error:", this may be due extraneous modules loaded into your environement that do not allow lis to run properly. View your modules using the command module list. If extraneous modules are loaded, run module purge to clear your environment and then module load [lisf module file] to load an environment suitable to running LISF. See the "discover_quick_start" document in the LISF Users' Guides for more information. +
@@ -2041,7 +2130,7 @@

Download Input and Target Files

-The tar file for this step is approximately 80MB compressed and 220MB unpacked. Ensure that you have enough storage available before downloading testcase files. +The tar file for this step is approximately 80MB compressed and 327MB unpacked. Ensure that you have enough storage available before downloading testcase files. @@ -2051,8 +2140,8 @@

Download Input and Target Files

-
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase6_lis_da_2020.tar.gz
-% tar -xzf testcase6_lis_da_2020.tar.gz -C .
+
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase6_lis_da_2023.tar.gz
+% tar -xzf testcase6_lis_da_2023.tar.gz -C .
@@ -2135,7 +2224,7 @@

The LIS Configuration File

Review the contents of lis.config_noah36_smapda to view the configuration settings used for the DA run:

-
Restart options
+
Restart options:
...
 Start mode:                                restart (1)
@@ -2150,7 +2239,7 @@ 
The LIS Configuration File

 
-
+
@@ -2163,7 +2252,7 @@ 
The LIS Configuration File

 

 1Select "restart" mode to use a restart file (compare with coldstart mode).Select "restart" mode to use a restart file (as opposed to "coldstart" mode).
 

 

 2
-
Data assimilation options
+
Data assimilation options:
...
 Number of data assimilation instances:               1
@@ -2183,7 +2272,7 @@ 
The LIS Configuration File
-
Scaling strategy options
+
Scaling strategy options:
...
 Data assimilation scaling strategy:         "CDF matching"
@@ -2198,7 +2287,7 @@ 
The LIS Configuration File
-
Perturbation options
+
Perturbation options:
...
 Perturbations start mode:                 "coldstart"
@@ -2239,7 +2328,7 @@ 
The LIS Configuration File
-
Observation data options
+
Observation data options:
SMAP(NASA) soil moisture data designation:       SPL3SMP
 SMAP(NASA) soil moisture data directory:        ./RS_DATA/SMAP/SPL3SMP.005
@@ -2414,6 +2503,7 @@ 
Run LIS - SMAP DA Experiment

 

 step 6 output example
 

+
SoilMoist_tavg variable in LIS_HIST_201701010600.d01.nc
@@ -2442,7 +2532,7 @@

Download Input and Target Files

-The tar file for this step is approximately 150KB compressed and 700KB unpacked. Ensure that you have enough storage available before downloading testcase files. +The tar file for this step is approximately 481KB compressed and 7.2MB unpacked. Ensure that you have enough storage available before downloading testcase files. @@ -2452,8 +2542,8 @@

Download Input and Target Files

-
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase7_lvt_expcomp_2020.tar.gz
-% tar -xzf testcase7_lvt_expcomp_2020.tar.gz -C .
+
% curl -O https://portal.nccs.nasa.gov/lisdata_pub/Tutorials/Web_Version/testcase7_lvt_expcomp_2023.tar.gz
+% tar -xzf testcase7_lvt_expcomp_2023.tar.gz -C .
@@ -2662,8 +2752,8 @@

Wrap Up

diff --git a/working_with_github/working_with_github.html b/working_with_github/working_with_github.html index b9a095458..e2cb0ad0a 100644 --- a/working_with_github/working_with_github.html +++ b/working_with_github/working_with_github.html @@ -2040,7 +2040,7 @@

9. Creating a release