Submitting GEOS-Chem support requests

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On this page we provide information about how to report any GEOS-Chem issues that you may encounter.

Contacting the GEOS-Chem Support Team for assistance

Please send all GEOS-Chem support requests to the GEOS-Chem Support Team (aka GCST) at: geos-chem-support [at] as.harvard.edu. This will send your request to all GCST members

What type of support can I expect?

The GCST is will be happy to assist you in resolving bugs and technical issues that may arise when compiling or running GEOS-Chem. User support and outreach is an important part of the GCST's mission to support the International GEOS-Chem User Community.

Even though the GCST assists users in many different ways, it cannot possibly do everything for everyone. GEOS-Chem users are expected to take on certain responsibilities. (For example, the GCST relies on users to make sure that their computer system has all of the software libraries needed to run GEOS-Chem.)

What information should I include?

Here is a quick list of information that you should send to the GCST when reporting an issue.


Item Description
LAST_COMMIT The location (aka "commit") of your source code in the Git version history. (You can use the gitk browser to view the Git version history.)
VERSION The GEOS-Chem version number.
MET The meteorology that is driving GEOS-Chem (e.g. geosfp, merra2).
GRID The horizontal grid (e.g. 4° x 5° , 2° x 2.5°, 0.25° x 0.3125°, 0.5° x 0.625°) that your simulation uses.
SIM The name of your GEOS-Chem simulation (e.g. Standard, Benchmark, CH4, Rn-Pb-Be, Hg, etc.).
NEST The nested region that your simulation uses (e.g. as, af, ch, na, eu, etc.). This only applies to nested-grid simulations.
COMPILER The compiler version that you used to build the GEOS-Chem executable file.

A description of the issue

Please include a brief description of the issue and any error messages that you encountered. Also include the steps (e.g. compile and run commands) that you used.

Of particular importance: The GEOS-Chem Support Team needs to know if you are using an unmodified (aka "out-of-the-box") version of GEOS-Chem, or if you have made any modifications to the code or input data. If you have modified GEOS-Chem, then please take a moment to doublecheck your modified code or data to make sure that it is not the source of the error.

The lastbuild file

The GEOS-Chem "Classic" compilation sequence generates a file that contains all of the options that were used to build the executable file. This file is named either lastbuild.mp (if OpenMP parallelization is turned on) or lastbuild.sp (if OpenMp parallelization is turned off).

Here is a sample lastbuild.mp file from a recent 1-month benchmark simulation:

LAST BUILD INFORMATION:
  CODE_DIR     : /n/home05/msulprizio/GC/Code.Dev
  CODE_BRANCH  : dev/12.1.0
  LAST_COMMIT  : Revert to reading I3 met fields each hour instead of once per day 
  COMMIT_DATE  : Wed Nov 21 09:07:51 2018 -0500 
  VERSION      : 12.1.0
  VERSION_TAG  : GC_12.1.0
  MET          : geosfp
  GRID         : 4x5
  SIM          : benchmark
  NEST         : n
  TRACEBACK    : y
  BOUNDS       : n
  DEBUG        : n
  FPE          : n
  NO_ISO       : n
  NO_REDUCED   : y
  CHEM         : Standard
  TOMAS12      : n
  TOMAS15      : n
  TOMAS30      : n
  TOMAS40      : n
  RRTMG        : n
  MASSCONS     : n
  TIMERS       : 1
  TAU_PROF     : n
  BPCH_DIAG    : y
  NC_DIAG      : y
  COMPILER     : ifort 17.0.4
  Datetime     : 2018/11/21 10:33       

At a very minimum, the GCST needs to know the following items in order to be able to diagnose your issue:

Item Description
LAST_COMMIT The location (aka "commit") of your source code in the Git version history. (You can use the gitk browser to view the Git version history.)
VERSION The GEOS-Chem version number.
MET The meteorology that is driving GEOS-Chem (e.g. geosfp, merra2).
GRID The horizontal grid (e.g. 4° x 5° , 2° x 2.5°, 0.25° x 0.3125°, 0.5° x 0.625°) that your simulation uses.
SIM The name of your GEOS-Chem simulation (e.g. Standard, Benchmark, CH4, Rn-Pb-Be, Hg, etc.).
NEST The nested region that your simulation uses (e.g. as, af, ch, na, eu, etc.). This only applies to nested-grid simulations.
COMPILER The compiler version that you used to build the GEOS-Chem executable file.

The GEOS-Chem log file

The GEOS-Chem Support Team will also need to look at the complete log file from your GEOS-Chem simulation. In many cases, GEOS-Chem users send us screenshots of the error message, but in practice this does not provide enough information to solve the problem.

The GEOS-Chem log file contains an "echo-back" of all input options, as well as a list of files that are being read in, and operations that are being done at each timestep. Here is an example log file from a recent 1-month benchmark simulation:

*************   S T A R T I N G   4 x 5   G E O S - C H E M   *************

===> Mode of operation         : GEOS-Chem "Classic"
===> GEOS-Chem version         : 12.1.0
===> Compiler                  : Intel Fortran Compiler (aka ifort)
===> Driven by meteorology     : GMAO GEOS-FP (on native 72-layer vertical grid)
===> ISORROPIA ATE package     : ON
===> Parallelization w/ OpenMP : ON
===> Binary punch diagnostics  : ON
===> netCDF diagnostics        : ON
===> netCDF file compression   : SUPPORTED

===> SIMULATION START TIME: 2018/11/21 10:38 <=== 

===============================================================================
G E O S - C H E M   U S E R   I N P U T 

READ_INPUT_FILE: Reading input.geos

SIMULATION MENU
---------------
Start time of run           : 20160701 000000
End time of run             : 20160801 000000
Run directory               : ./
Data Directory              : /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/
CHEM_INPUTS directory       : /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/CHEM_INPUTS/
Resolution-specific dir     : GEOS_4x5/
Is this a nested-grid sim?  :     F
Global offsets I0, J0       :     0    0

TIMESTEP MENU
---------------
Transport/Convection [sec]  :   600
Chemistry/Emissions  [sec]  :  1200 

... etc ...

If your simulation stopped with an error, a detailed error message should also appear in the GEOS-Chem log file.

The HEMCO log file

The HEMCO emissions component also produces a log file. The log file is named HEMCO.log. The HEMCO log file contains information about how emissions, met fields, and other relevant data are read from disk and processed for input into GEOS-Chem.

(NOTE: When your simulation finishes successfully, the HEMCO.log file is automatically renamed to either HEMCO.log.mp (if OpenMP parallelization is turned on) or HEMCO.log.sp (if OpenMP parallelization is turned off). But if your run dies with an error, the HEMCO log file will not have been renamed.)

Here is a sample HEMCO.log file from a recent 1-month benchmark simulation (edited for brevity):

-------------------------------------------------------------------------------
Using HEMCO v2.1.010    
-------------------------------------------------------------------------------
Registering HEMCO species:
Species NO
Species O3
Species PAN
Species CO
... etc ...

-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Use air-sea flux emissions (extension module)
   - Use species:
    - DMS          25
    - ACET           9
    - ALD2          11
-------------------------------------------------------------------------------
Use ParaNOx ship emissions (extension module)
    - Use the following species: (MW, emitted as HEMCO ID)
     NO  : 30.00    1
     NO2 : 46.00   64
     O3  : 48.00    2
     HNO3: 63.00    7
READ_LUT_NCFILE: Reading /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/HEMCO/PARANOX/v2015-02/ship_plume_lut_02ms.nc
READ_LUT_NCFILE: Reading /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/HEMCO/PARANOX/v2015-02/ship_plume_lut_06ms.nc
READ_LUT_NCFILE: Reading /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/HEMCO/PARANOX/v2015-02/ship_plume_lut_10ms.nc
READ_LUT_NCFILE: Reading /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/HEMCO/PARANOX/v2015-02/ship_plume_lut_14ms.nc
READ_LUT_NCFILE: Reading /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/HEMCO/PARANOX/v2015-02/ship_plume_lut_18ms.nc
-------------------------------------------------------------------------------
Use lightning NOx emissions (extension module)
  - Use species NO->           1
  - Use OTD-LIS factors from file?  T
  - Use GEOS-5 flash rates:  F
  - Use scalar scale factor:    1.000000
  - Use gridded scale field: none
     - INIT_LIGHTNOX: Reading /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/HEMCO/LIGHTNOX/v2014-07/light_dist.ott2010.dat
-------------------------------------------------------------------------------
Use soil NOx emissions (extension module)
    - NOx species            : NO           1
    - NOx scale factor       :    1.000000
    - NOx scale field        : none
    - Use fertilizer NOx     :  T
    - Fertilizer scale factor:   6.800000090152025E-003
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Use DEAD dust emissions (extension module)
Use the following species (Name: HcoID):
 DST1:          38
 DST2:          39
 DST3:          40
 DST4:          41
 Global mass flux tuning factor:   8.328599999999999E-004
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Use sea salt aerosol emissions (extension module)
 Accumulation aerosol: SALA:          42
  - size range       :   1.000000000000000E-002  0.500000000000000
  Coarse aerosol      : SALC:          43
  - size range       :   1.000000000000000E-002  0.500000000000000
  - wind scale factor:    1.00000000000000
-------------------------------------------------------------------------------
Use MEGAN biogenic emissions (extension module)
-------------------------------------------------------------------------------
  - This is instance            1
 - Use the following species:
    Isoprene   = ISOP           6
    Acetone    = ACET           9
    C3 Alkenes = PRPE          18
    Ethene     = C2H4          -1
    ALD2       = ALD2          11
    EOH        = EOH          96
  SOA-Precursor = SOAP          94
  SOA-Simple  = SOAS          95
  --> Isoprene scale factor is    1.00000000000000
  --> Use CO2 inhibition on isoprene option  T
  --> Global atmospheric CO2 concentration :    390.000000000000       ppmv
  --> Normalize LAI by PFT:  T
 - MEGAN monoterpene option enabled
    CO         = CO           4
      a-,b-pinene    = MTPA          70
      Other monoterp.= MTPO          72
      Limonene       = LIMO          71
      Sesquiterpenes = SESQ         184
-------------------------------------------------------------------------------
Use GFED extension
    - Use GFED-4              :  T
    - Use daily scale factors :  F
    - Use hourly scale factors:  F
    - Hydrophilic OC fraction :   0.5000000
    - Hydrophilic BC fraction :   0.2000000
    - POG1 fraction           :   0.4900000
    - SOAP fraction           :   1.3000000E-02
   - Emit GFED species NO     as model species NO
      --> Will use scale factor:    1.000000
      --> Will use scale field : none
   - Emit GFED species CO     as model species CO
      --> Will use scale factor:    1.050000
     --> Will use scale field : none
   ... etc...
 
-------------------------------------------------------------------------------
HEMCO v2.1.010 FINISHED.
Warnings (level 1 or lower):  25386
-------------------------------------------------------------------------------

--Bob Yantosca (talk) 16:16, 29 November 2018 (UTC)

The job output file from the batch scheduler

slurm-60034556.out