[PULL REQUEST] Bug fixes for GEOS-Chem Classic dry-run simulations #661
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
The State_Chm%HetInfo and State_Diag%SpeciesBC fields were never set to NULL during initialization. While this is OK for most simulations, when doing a dry-run simulation, this will cause deallocation to fail, at least when using GNU Fortran. This would cause a segmentation fault at the end of dry-run simulations (but the dry-run simulations would finish otherwise OK). Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
File reads have been moved out of the INIT_UCX routine, but there were still some print statements left over. These print statements would write that a non-existent file was missing, thus causing dry-runs to fail. We have now removed these extraneous print statements. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
Here we are stashing some modifications to download_data.py for downloading restart files for GEOS-Chem 13.0.0. Will need to work on this further... Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
The NOON_FILE_ROOT variable was a module variable that was removed in the prior commit 991ca72. However, this variable is needed to read in the UCX boundary conditions in routine NOXCOEFF_INIT. We have now restored NOON_FILE_ROOT as a local variable to NOXCOEFF_INIT. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
(1) run/GCClassic/createRunDir.sh: - Aerosol simulations now use the fullchem restart file - POPs simulation now looks for an initial restart file w/ the extra option (BaP, PYR, PHE) in ExtData/GEOSCHEM_RESTARTS/v2020-02 - All other specialty simulations use restart files in GEOSCHEM_RESTARTS/v2020-02 on the remote server - Send error output from aws s3 cp to dev/null (2) run/shared/download_data.py - Look for NK15 and NK40 in input.geos to decide if we are need to download data files for TOMAS15 and TOMAS40 simulations - Use the fullchem restart file (Jan 2019) for the aerosol simulation - Look for specialty simulation restart files in GEOSCHEM_RESTARTS/v2020-02 - When downloading data from ComputeCanada, first download it to the local GEOSCHEM_RESTARTS directory tree, then copy it to the run directory. - AWS restart files should now be placed in the run directory by createRunDir.sh. But if a restart file is missing, running download_data.py with -aws will restore it. NOTE: There may still be an issue with the POPs restart files on AWS, but since POPs is not used by many people I am not sure if we want to end up fixing this. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
yantosca
added
category: Bug
msulprizio
approved these changes
Mar 22, 2021
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Overview
This PR fixes several issues in the GEOS-Chem "Classic" dry-run simulation, namely:
Routine
INIT_UCXin (GeosCore/ucx_mod.F90), was printing incorrect dry-run output to the log file, which caused dry-run simulations to hang. This has now been corrected.The
run/GCClassic/createRunDir.shscript has the following updates:a. Aerosol simulations now use the fullchem restart file
b. POPs simulation now looks for an initial restart file w/ the extra option (BaP, PYR, PHE) in
ExtData/GEOSCHEM_RESTARTS/v2020-02.c. All other specialty simulations use restart files in
GEOSCHEM_RESTARTS/v2020-02on the remote serverd. Send error output from
aws s3 cptodev/nullThe
run/shared/download_data.pyscript has the following updates:a. Look for NK15 and NK40 in input.geos to decide if we need to download data files for TOMAS15 and TOMAS40 simulations
b. Use the fullchem restart file (Jan 2019) for the aerosol simulation
c. Look for specialty simulation restart files in
GEOSCHEM_RESTARTS/v2020-02d. When downloading data from ComputeCanada, first download it to the local
GEOSCHEM_RESTARTSdirectory tree, then copy it to the run directory.e. AWS restart files should now be placed in the run directory by
createRunDir.sh. But if a restart file is missing, runningdownload_data.pywith-awswill restore it.In
state_chm_mod.F90, we now nullify theState_Chm%HetInfoandState_Chm%Map_SpeciesBCfields in routineInit_State_Chm. Explicitly setting these fields toNULL()will make them be recognized as unallocated by the compiler, which can prevent seg faults during finalization, at least with the later GNU Fortran compilers.Also note: 2 x 2.5 specialty simulation restart files have been copied to
ExtData/GEOSCHEM_RESTARTS/v2020-02. The reference time of these restart files has been edited to either 2019-01-01 or 2019-07-01.Testing
The dry-run capability was tested on the AWS cloud. The proper restart files are now being placed into the run directories.
CAVEAT: There may be still some issues with the POPS simulation, since there are 3 separate restart files. But since the POPs simulation is basically unused, I think we can address any user-reported issues that come up on a case-by-case basis.