GEOS-Chem log files

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  1. Minimum system requirements
  2. Configuring your computational environment
  3. Downloading source code
  4. Downloading data directories
  5. Creating run directories
  6. Configuring runs
  7. Compiling
  8. Running
  9. Output files
  10. Visualizing and processing output
  11. Coding and debugging
  12. Further reading


Overview

On this page we provide information about the various log file output that GEOS-Chem produces.

List of log files produced by GEOS-Chem

File(s) Format Description Notes
compile.log Text The compile.log file. Contains echo-back of the GEOS-Chem compilation output. Can be useful for debugging. Introduced in 12.6.0.

Please include this file when submitting a GEOS-Chem support request.

lastbuild Text The lastbuild file. Contains a summary of all of the options that were used to build the GEOS-Chem executable. This file is created each time you compile GEOS-Chem. Please include this file when submitting a GEOS-Chem support request.
GC_*.log Text The GEOS-Chem log file. Contains an "echo-back" of all input options that were specified in input.geos, the list of diagnostic quantities that are being archived, the list of files that are being read, and information about the operations that are being done at each GEOS-Chem timestep. If you run dies with an error, a detailed error message should be printed here. Please include this file when submitting a GEOS-Chem support request.
log.dryrun
or similar names
Text The GEOS-Chem log file with dry-run output. Contains the full path names of all input files (configuration files, meteorology files, emissions files) that are read by GEOS-Chem. This will allow users to download only those files that their GEOS-Chem simulation requires, thus speeding up the data downloading process. The GEOS-Chem dry-run option will be available in GEOS-Chem 12.7.0 and later versions.
HEMCO.log Text The HEMCO log file. Contains information about how emissions, met fields, and other relevant data are read from disk and processed by HEMCO for input into GEOS-Chem. Please include this file when submitting a GEOS-Chem support request.
slurm-JOBID.out Text The job output file. If you used a batch scheduler such as SLURM, PBS, LSF, etc. to submit your GEOS-Chem simulation, then output from the Unix stdout and/or stderr streams may be printed to this file. This file may contain important error messages. Please include this file when submitting a GEOS-Chem support request.

--Bob Yantosca (talk) 16:19, 30 November 2018 (UTC)

In-depth description of GEOS-Chem log files

compile.log file

This file is created by the compilation process in GEOS-Chem 12.6.0 and later versions. It contains an echo-back of all of the commands used to compile each file.

make[1]: Entering directory `/local/ryantosca/GC/Code.Dev'
make[2]: Entering directory `/local/ryantosca/GC/Code.Dev/GeosCore'
make[3]: Entering directory `/local/ryantosca/GC/Code.Dev/GeosCore'
make[4]: Entering directory `/local/ryantosca/GC/Code.Dev/GeosCore'
make[5]: Entering directory `/local/ryantosca/GC/Code.Dev/NcdfUtil'
gfortran -cpp -w -std=legacy -fautomatic -fno-align-commons -fconvert=big-endian ... charpak_mod.F90
gfortran -cpp -w -std=legacy -fautomatic -fno-align-commons -fconvert=big-endian ... julday_mod.F
gfortran -cpp -w -std=legacy -fautomatic -fno-align-commons -fconvert=big-endian ... m_do_err_out.F90
...etc...

NOTE: This output can be very long (several hundred characters per line). We have truncated it to fit into the wiki window.

--Bob Yantosca (talk) 19:13, 20 December 2019 (UTC)

GEOS-Chem log file

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.

--Bob Yantosca (talk) 17:13, 30 November 2018 (UTC)

GEOS-Chem log file with dry-run output

NOTE: The dry-run option will be available in GEOS-Chem 12.7.0 and later versions

The GEOS-Chem log file with dry-run output looks similar regular GEOS-Chem log file. There are extra output headers to let you know that this log file was produced by a dry-run simulation, which generated no output. The complete path name of each file is printed, along with information whether the file was found ("Opening") or not found ("REQUIRED FILE NOT FOUND") on disk.

You can use the download_data.py Python script in the GEOS-Chem run directory to:

  1. Parse this information into a list of "unique" file names (i.e. with all duplicates removed), and
  2. Download data from either Compute Canada or AWS cloud storage to your computer system or cloud instance.

For more information, please see our Downloading data with the GEOS-Chem dry-run option wiki page.

Here are some snippets from a GEOS-Chem log file with dry-run output:

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

===> Mode of operation         : GEOS-Chem "Classic"
===> GEOS-Chem version         : 12.7.0
===> Compiler                  : GNU Fortran compiler (aka gfortran)
===> Parallelization w/ OpenMP : ON
===> Binary punch diagnostics  : OFF
===> netCDF diagnostics        : ON
===> netCDF file compression   : SUPPORTED
===> Luo et al (2019) wetdep?  : OFF

===> SIMULATION START TIME: 2019/12/13 12:40 <===

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

READ_INPUT_FILE: Opening ./input.geos

 ... etc ...
 
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!! GEOS-CHEM IS IN DRY-RUN MODE!
!!!
!!! You will NOT get output for this run!
!!! Use this command to validate a GEOS-Chem run configuration:
!!!   ./geos --dryrun > log
!!!
!!! REMOVE THE --dryrun ARGUMENT FROM THE COMMAND LINE
!!! BEFORE RUNNING A GEOS-Chem PRODUCTION SIMULATION!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!! Start Date       : 20160701 000000
!!! End Date         : 20160701 010000
!!! Simulation       : benchmark
!!! Meteorology      : GEOSFP
!!! Grid Resolution  : 4.0x5.0
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

... etc ...
HEMCO (INIT): Opening ./HEMCO_Config.rc
HEMCO (INIT): Opening ./HEMCO_Diagn.rc
HEMCO: Opening /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/HEMCO/EDGARv43/v2016-11/EDGAR_v43.BC.POW.0.1x0.1.nc

... etc ...

HEMCO: REQUIRED FILE NOT FOUND /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/HEMCO/EDGARv43/v2016-11/EDGAR_v43.BC.POW.0.1x0.1.nc

... etc ...

--Bob Yantosca (talk) 17:51, 13 December 2019 (UTC)

HEMCO log file

The HEMCO emissions component also produces a log file, which 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
-------------------------------------------------------------------------------

For more information, please see The HEMCO User's Guide.

--Bob Yantosca (talk) 22:22, 12 December 2019 (UTC)

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      

The GEOS-Chem Support Team will need to see the following fields of the lastbuild file in order to assist you in resolving bugs or technical issues that you might encounter.

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.

--Bob Yantosca (talk) 22:23, 12 December 2019 (UTC)



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