Grdmat failed when running smk_edgar_HEMI108k.csh


#1

Hi~I am using SMOKEv4.0 and included EDGAR data. But when I try to run smk_edgar_HEMI108k.csh, the logs file show grdmat is not completed. here is my grdmat.edgar.HEMI_108k.NH108k.log

This program uses the EPA-AREAL/MCNC-EnvPgms/BAMS Models-3      
 I/O Applications Programming Interface, [I/O API] which is      
 built on top of the netCDF I/O library (Copyright 1993, 1996    
 University Corporation for Atmospheric Research/Unidata         
 Program) and the PVM parallel-programming library (from         
 Oak Ridge National Laboratory).                                 
 Copyright (C) 1992-2002 MCNC,                                   
 (C) 1992-2013 Carlie J. Coats, Jr.,                             
 (C) 2003-2012 Baron Advanced Meteorological Systems, LLC, and   
 (C) 2014-2016 UNC Institute for the Environment.                
 Released under the GNU LGPL  License, version 2.1.  See URL     
                                                                 
     https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html     
                                                                 
 for conditions of use.  

 ioapi-3.2: $Id: init3.F90 320 2016-02-26 15:55:00Z coats $
 Version with PARMS3.EXT/PARAMETER::MXVARS3= 2048
 netCDF version "3.6.3" of Mar 16 2016 10:20:39 $
  
  
 Missing environment variable EXECUTION_ID
 SMOKE ---------------
 Copyright (c)2004 Environmental Modeling for Policy Development
 All rights reserved

 Program GRDMAT, Version SMOKEv40_Sep2015
 Online documentation 
     http://www.cep.unc.edu/empd/products/smoke                 
  
 Program GRDMAT to take a SMOKE area, mobile, or point source
 inventory file, gridding surrogates,  surrogate cross-
 reference, and an optional link definitions file, and produce
 a SMOKE gridding matrix for a grid defined at run time. For
 mobile sources, an "ungridding" matrix is also created to
 allow the use of gridded temperature data in assigning
 factors to mobile sources.
  
  
 You will need to enter the logical names for the input and
 output files (and to have set them prior to program start,
 using "setenv <logicalname> <pathname>").
  
 You may use END_OF-FILE (control-D) to quit the program
 during logical-name entry. Default responses are given in
 brackets [LIKE THIS] and can be accepted by hitting the
 <RETURN> key.
  
 Value for PROMPTFLAG:  N returning FALSE
 Returning default value TRUE for query:
 "Continue with program?"
 Value for GRDMAT_ADJUST not defined;returning default:   FALSE
 Value for GRDMAT_LINKDEFS not defined;returning default:   FALSE
 Value for USE_VARIABLE_GRID not defined;returning default:   FALSE
 Value for IMPORT_GRDNETCDF_YN:  Y returning TRUE
 Value for SMK_SOURCE:  'A'
 Value for SMK_SOURCE:  'A'
 Value for PROMPTFLAG:  N returning FALSE

 File "AREA" opened for input on unit:  98
 /home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/area.map.edgar.HEMI_108k.txt

 Value for AREA:  '/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/area.map.edgar.HEMI_108k.txt'
 Value for AREA:  '/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/area.map.edgar.HEMI_108k.txt'

 File "ASRC" opened for input on unit:  97
 /home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgarsrc.HEMI_108k.txt

 Value for IOAPI_CHECK_HEADERS not defined;returning default:   FALSE
  
 "AREA" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 6480000 rows, 1 cols, 1 lays, 4 vbles
 NetCDF ID:         6  opened as READONLY            
 Time-independent data.
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/CO.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 1087264 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/NH3.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 1078304 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/NOX.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 1087658 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/PM10.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 1086698 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/PM2_5.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 1086591 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/SO2.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 1086050 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/VOC.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 1086621 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/PMC.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 677872 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/CO.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 1087264 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/NH3.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 1078304 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/NOX.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 1087658 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/PM10.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 1086698 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/PM2_5.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 1086591 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/SO2.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 1086050 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/VOC.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 1086621 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
  
 "TMP_POL_FILE" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/inventory/HEMI_108k/edgar.HEMI_108k_dat/PMC.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name ""
 Dimensions: 677872 rows, 1 cols, 1 lays, 7 vbles
 NetCDF ID:         7  opened as READONLY            
 Time-independent data.
 Closing file TMP_POL_FILE
 Reading source data from inventory file...
 Value for GRIDDESC:  '/home/xiao/Build_WRF/smoke/data/ge_dat/GRIDDESC'
 Value for GRIDDESC:  '/home/xiao/Build_WRF/smoke/data/ge_dat/GRIDDESC'

 File "GRIDDESC" opened for input on unit:  96
 /home/xiao/Build_WRF/smoke/data/ge_dat/GRIDDESC

 WARNING: Line         1 in GRIDDESC file skipped because more than 32 fields were found.
 Value for IOAPI_GRIDNAME_1:  'HEMI_108k'
 Value for IOAPI_GRIDNAME_1:  'HEMI_108k'

 File "GRIDDESC" opened for input on unit:  96
 /home/xiao/Build_WRF/smoke/data/ge_dat/GRIDDESC

 NOTE: Grid settings initialized using HEMI_108k        in  
      grid description file.
 NOTE: Output grid "HEMI_108k" set; described as 
      No description available
 Value for IOAPI_GRIDNAME_1:  'HEMI_108k'
 Value for IOAPI_GRIDNAME_1:  'HEMI_108k'

 File "AGSUP" opened for output on unit:  96
 /home/xiao/Build_WRF/smoke/data/run_HEMI_108k/static/agsup.edgar.NH108k.HEMI_108k.txt

 Generating gridding matrix...
  
 "GRIDMASK" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/ge_dat/EDGAR/GRIDMASK_EDGAR.ncf"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name "LATLON_EDGAR0.1"
 Dimensions: 1800 rows, 3600 cols, 1 lays, 2 vbles
 NetCDF ID:         8  opened as READONLY            
 Time-independent data.
  
 "GRID_CRO_2D" opened as OLD:READ-ONLY   
 File name "/home/xiao/Build_WRF/smoke/data/met/run_108km/GRIDCRO2D"
 File type GRDDED3 
 Execution ID "????????????????"
 Grid name "WRF_CMAQ_2WAY"
 Dimensions: 187 rows, 187 cols, 1 lays, 27 vbles
 NetCDF ID:         9  opened as READONLY            
 Time-independent data.
 
 Processing coordinate transforms...
 
 Value for IOAPI_ISPH:  '20'
 Value for IOAPI_ISPH:  '20'
 INITSPHERES:  input sphere Normal Sphere (MM5 / WRF-ARW) R=6370000
 
 Processing coordinate transforms...
 
 This file seems to use WMO-style "longitude" that violates ISO Standard 6709
 Number of coeffs   3661962

Does anyone know how to fix this? Thanks in advance


#2

smkinven and spcmat are completed. temporal and smkmerge failed, because of the grdmat failure I guess. And one error in smkmerge log file is ‘Could not open file set “ATMP”.’


#3

It’s conceivable you’re running into a memory-model problem (many compilers even in 64-bit Linux generate code that uses 32-bit pointers by default, and I’ve seen programs that use too-big arrays or too much stack "go off into never-never-land when built this way).

See what happens if you build everything (from the libraries on up) with the “medium” memory model. See the I/O API manual’s section on this:
https://www.cmascenter.org/ioapi/documentation/all_versions/html/AVAIL.html#medium
or https://cjcoats.github.io/ioapi/AVAIL.html#medium


#4

Thanks so much for your reply! You are right, and the problem is caused by the limited stacksize. I added ‘limit the stacksize unlimited’ in the script smk_edgar_HEMI108k.csh. The problem is solved.