Comments (13)
This is happening in Chem_GridCompMod.F90:
! Set spc conc to background value if rst skipped or var not there
IF ( RC /= ESMF_SUCCESS .OR. RST == MAPL_RestartBootstrap .OR. &
RST == MAPL_RestartSkipInitial ) THEN
DO L = 1, LLPAR
DO J = 1, JJPAR
DO I = 1, IIPAR
! Special handling for MOH (mimicking GEOS-Chem Classic)
IF ( TRIM( ThisSpc%Name ) == 'MOH' ) THEN
! Test for altitude (L < 9 is always in the trop)
IF ( L <= 9 ) THEN
! Test for ocean/land boxes
IF ( State_Met%FRCLND(I,J) >= 0.5 ) THEN
! Continental boundary layer: 2 ppbv MOH
State_Chm%Species(I,J,L,IND) = 2.000e-9_fp
ELSE
! Marine boundary layer: 0.9 ppbv MOH
State_Chm%Species(I,J,L,IND) = 0.900e-9_fp
ENDIF
ELSE
! Test for troposphere
IF ( State_Met%InTroposphere(I,J,L) ) THEN
! Free troposphere: 0.6 ppbv MOH
State_Chm%Species(I,J,L,IND) = 0.600e-9_fp
ELSE
! Strat/mesosphere:
State_Chm%Species(I,J,L,IND) = 1.0E-30_FP
ENDIF
ENDIF
ELSEIF ( L > LLCHEM .AND. &
( .NOT. ThisSpc%Is_Advected ) ) THEN
! For non-advected spc at L > LLCHEM, use small number
State_Chm%Species(I,J,L,IND) = 1.0E-30_FP
ELSE
! For all other cases, use the background value in spc db
State_Chm%Species(I,J,L,IND) = ThisSpc%BackgroundVV
ENDIF
ENDDO
ENDDO
ENDDO
Ptr3D_R8(:,:,:) = State_Chm%Species(:,:,LM:1:-1,IND)
IF ( MAPL_am_I_Root()) THEN
WRITE(*,*) &
' WARNING: using background values from species database'
ENDIF
ENDIF
Maybe the warning message is useless by now and we could remove it. Did this come in with the GEOS-5 updates?
from gchp_legacy.
I have not been able to reproduce these warning messages for advected species using a full chemistry simulation with GCHP on the Odyssey cluster. I only get these messages for internal state variables NOT in the restart file, such as recently added species pFe and HEMCO restart variables. This indicates the warnings are being issued correctly for my particular run. This code was put into GCHP in March 2018 and was not part of a GEOS-5 update.
I notice that your log file includes messages like this for every single internal state variable:
Bootstrapping Variable: SPC_NMAO3 in initial_GEOSChem_rst.c24_standard.nc
Bootstrapping Variable: SPC_NO in initial_GEOSChem_rst.c24_standard.nc
Bootstrapping Variable: SPC_NO2 in initial_GEOSChem_rst.c24_standard.nc
Bootstrapping Variable: SPC_NO3 in initial_GEOSChem_rst.c24_standard.nc
Bootstrapping Variable: SPC_NPMN in initial_GEOSChem_rst.c24_standard.nc
If the restart file is read correctly then you should see a much shorter list, specifically this in 12.1.0, just with the restart filename swapped out:
Using parallel NetCDF for file: initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: ARCHV_DRY_TOTN in initial_GEOSChem_rst.c48_benchmark.
nc
Bootstrapping Variable: ARCHV_WET_TOTN in initial_GEOSChem_rst.c48_benchmark.
nc
Bootstrapping Variable: DEP_RESERVOIR in initial_GEOSChem_rst.c48_benchmark.n
c
Bootstrapping Variable: DRYPERIOD in initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: GCCTROPP in initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: GWET_PREV in initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: LAI_PREVDAY in initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: PARDF_DAVG in initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: PARDR_DAVG in initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: PFACTOR in initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: SPC_LCH4 in initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: SPC_LOx in initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: SPC_PH2O2 in initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: SPC_POx in initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: SPC_pFe in initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: STATE_PSC in initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: T_DAVG in initial_GEOSChem_rst.c48_benchmark.nc
Bootstrapping Variable: T_PREVDAY in initial_GEOSChem_rst.c48_benchmark.nc
Based on code in Chem_GridCompMod right before the conditional in which the background value warning message is issued, it appears that the call to ESMF_AttributeGet for the 'RESTART' attribute is returning MAPL_RestartBootstrap which is one of the conditions that will lead to using background values from the species database. We know the attribute is that value due to the bootstrapping warnings that are in the log file. Those warnings, along with the restart attribute per internal state variable, were created by MAPL earlier in the execution.
! Determine if species in restart file
CALL ESMF_StateGet( INTERNAL, TRIM(SPFX) // TRIM(ThisSpc%Name), &
trcFIELD, RC=RC )
CALL ESMF_AttributeGet( trcFIELD, NAME="RESTART", &
VALUE=RST, RC=STATUS )
! Set spc conc to background value if rst skipped or var not there
IF ( RC /= ESMF_SUCCESS .OR. RST == MAPL_RestartBootstrap .OR. &
RST == MAPL_RestartSkipInitial ) THEN
Check that your restart file exists in the run directory and contains the content you think it does.
from gchp_legacy.
Found the issue.
I was using the latest GEOSCHEM_RESTARTS/v2018-11/initial_GEOSChem_rst.c24_standard.nc
, which uses variable name SpeciesRst_O3
, but GCHP 12.1.0 still looks for SPC_O3
. Using the old restart file GEOSCHEM_RESTARTS/v2016-07/initial_GEOSChem_rst.c24_standard.nc
fixes the problem.
from gchp_legacy.
Oops the situation actually gets worse.
With the "proper" restart file v2016-07/initial_GEOSChem_rst.c24_standard.nc
, the simulation always crashes at hour 1 (when the diagnostics first get written), even if I set the simulation period to 2 days. This is the default setting in ami-0a5973f14aad7413a
The simulation is able to proceed with the "improper" restart file v2018-11/initial_GEOSChem_rst.c24_standard.nc
. This is the default setting in ami-0f44e999c80ef6e66
.
from gchp_legacy.
We should delete any GCHP restart files that are in that folder since the older files should be used instead. I will replace them with symbolic links to the older files in case people go to that folder looking for restarts. We do not plan on changing the internal state name in GCHP so SPC_ is the correct name to use. Thanks for reporting that!
Could you provide your log file for your latest run problem?
from gchp_legacy.
Hi all! I agree with Lizzie and I meant to do that earlier. Sorry I dropped the ball. I'll fix it now.
from gchp_legacy.
Okay, see this new issue and the logs are posted in geoschem/GCHP#6. Let's keep the discussion of that issue to here rather than in two places. The printing of timing values issue is unrelated.
from gchp_legacy.
The GCHP restart files are now removed from ExtData/GEOSCHEM_RESTARTS/v2018-11.
It may take a while to sync to the Harvard ftp and to AWS.
from gchp_legacy.
Thanks Melissa! Jiawei, try turning off all collections. If that works, then turn on one collection, e.g. SpeciesConc, and check if results are okay. If that all works please open a new issue related to writing multiple files on the cloud.
from gchp_legacy.
I logged into the cloud with AMI: GCHP12.1.0_tutorial_20181210 (ami-0f44e999c80ef6e66)
When I run with all collections turned, off, I get an error in offline tracer advection at 00:10 into the run.
When I run with only SpeciesConc_avg and SpeciesConc_inst turned on, then we still get the bad termination error right after the GIGCenv time is printed out.
Will dig a bit further.
from gchp_legacy.
@yantosca Thanks for looking into this! I have the same finding, which is quite weird:
- 0 output: crashes at 00:10
- 1, 2, 3 outputs (Choose from
SpeciesConc_avg
,SpeciesConc_inst
,StateMet_avg
): proceeds and generates output files without problems. The final timing info is incomplete, but it is a separate issue. - 4 outputs (
SpeciesConc_avg
,SpeciesConc_inst
,StateMet_avg
,StateMet_inst
): crashes at 01:00 when writing the first output. This can be "solved" by using the incorrect restart filev2018-11
, for unknown reasons.
from gchp_legacy.
from gchp_legacy.
Agreed @lizziel
from gchp_legacy.
Related Issues (20)
- [BUG/ISSUE] Incorrect regridding if file latitude data ends in +/- 90 HOT 4
- [BUG/ISSUE] Not printing the missing HEMCO data file that causes model crash HOT 13
- [BUG/ISSUE] Change in MAPL vertical flip rules impacting mesospheric chemistry HOT 1
- [BUG/ISSUE] H2O2AfterChem vertically flipped in restart HOT 2
- [BUG/ISSUE] MODIS LAI not properly updated at correct time HOT 6
- [BUG/ISSUE] Run failure in transport tracers simulation with 12.6.2 HOT 1
- [FEATURE REQUEST] ESMF v8 public release HOT 1
- [BUG/ISSUE] Run crashes in MAPL when running full chemistry simulation at c360 HOT 6
- [QUESTION]Should it make cleanup_output everytime at the beginging of smulation? HOT 4
- [BUG/ISSUE] Fullchem run failure in 12.7.0+ at c180+ due to reduced timesteps HOT 4
- [DISCUSSION] This repository will be retired in version 13.0.0
- [BUG/ISSUE] Monthly diagnostics incorrect for Feb in leap years if using multi-run option HOT 1
- [QUESTION] Error in MAPL_IO.F90 reading restart file?
- [BUG/ISSUE]Invoking MPI_ABORT causes Open MPI to kill all MPI processes when run GCHP at c360 HOT 9
- [BUG/ISSUE]make build_all, gchp error in ESMF: cpp/node/detail/node_iterator.h(64): error: namespace "std" has no member "addressof" HOT 2
- [BUG/ISSUE] compiling GCHP 12.8.2 HOT 8
- [QUESTION] Compiling GCHP failed HOT 5
- [BUG/ISSUE] Non-advected species concentrations not copied for output restart file
- [QUESTION] The dimensions of gchp restart file HOT 3
- [QUESTION] Why does GCHP fail when meteorology turned on in 12.9.3 HEMCO_Config.rc HOT 4
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from gchp_legacy.