AE Namelist error in CMAQv5.2 one day benchmark

Jsward · October 18, 2018, 6:42pm

Hello all,

I am attempting to benchmark CMAQv5.2 on a new system using gcc and openmpi. All the execuatables have compiled, and ICON & BCON both run correctly. However, CCTM fails with the following AE namelist errors.

"INIT_AERO_1" opened as OLD:READ-ONLY   
 File name "/home/jas983/models/cmaq/CMAQ_v5.2/data/SE52BENCH/single_day/magma_output/icon/ICON_v52_SE52BENCH_profile"
 File type GRDDED3 
 Execution ID "ICON_v52_profile.exe"
 Grid name "SE52BENCH"
 Dimensions: 80 rows, 100 cols, 35 lays, 76 vbles
 NetCDF ID:    262144  opened as READONLY            
 Time-independent data.

 IC/BC Factors used for transported aerosol species
  38  ASO4J              1.0000    
  39  ASO4I              1.0000    
 No IC found for species ANH4J in INIT_AERO_1; set to  1.00E-30
 No IC found for species ANH4I in INIT_AERO_1; set to  1.00E-30
 No IC found for species ANO3J in INIT_AERO_1; set to  1.00E-30
 No IC found for species ANO3I in INIT_AERO_1; set to  1.00E-30
 No IC found for species AALK1J in INIT_AERO_1; set to  1.00E-30
 No IC found for species AALK2J in INIT_AERO_1; set to  1.00E-30
  40  AXYL1J             1.0000    
  41  AXYL2J             1.0000    
  42  AXYL3J             1.0000    
  43  ATOL1J             1.0000    
  44  ATOL2J             1.0000    
  45  ATOL3J             1.0000    
  46  ABNZ1J             1.0000    
  47  ABNZ2J             1.0000    
  48  ABNZ3J             1.0000    
 No IC found for species APAH1J in INIT_AERO_1; set to  1.00E-30
 No IC found for species APAH2J in INIT_AERO_1; set to  1.00E-30
 No IC found for species APAH3J in INIT_AERO_1; set to  1.00E-30
  49  ATRP1J             1.0000    
  50  ATRP2J             1.0000    
  51  AISO1J             1.0000    
  52  AISO2J             1.0000    
  53  ASQTJ              1.0000    
 No IC found for species AORGCJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species AECJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species AECI in INIT_AERO_1; set to  1.00E-30
 No IC found for species AOTHRJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species AOTHRI in INIT_AERO_1; set to  1.00E-30
 No IC found for species AFEJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species AALJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species ASIJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species ATIJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species ACAJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species AMGJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species AKJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species AMNJ in INIT_AERO_1; set to  1.00E-30
  54  ACORS              1.0000    
  55  ASOIL              1.0000    
  56  NUMATKN            1.0000    
  57  NUMACC             1.0000    
  58  NUMCOR             1.0000    
  59  SRFATKN            1.0000    
  60  SRFACC             1.0000    
  61  SRFCOR             1.0000    
 No IC found for species AH2OJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species AH2OI in INIT_AERO_1; set to  1.00E-30
 No IC found for species AH3OPJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species AH3OPI in INIT_AERO_1; set to  1.00E-30
 No IC found for species ANAJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species ANAI in INIT_AERO_1; set to  1.00E-30
 No IC found for species ACLJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species ACLI in INIT_AERO_1; set to  1.00E-30
 No IC found for species ASEACAT in INIT_AERO_1; set to  1.00E-30
 No IC found for species ACLK in INIT_AERO_1; set to  1.00E-30
 No IC found for species ASO4K in INIT_AERO_1; set to  1.00E-30
 No IC found for species ANH4K in INIT_AERO_1; set to  1.00E-30
 No IC found for species ANO3K in INIT_AERO_1; set to  1.00E-30
 No IC found for species AH2OK in INIT_AERO_1; set to  1.00E-30
 No IC found for species AH3OPK in INIT_AERO_1; set to  1.00E-30
  62  AISO3J             1.0000    
  63  AOLGAJ             1.0000    
  64  AOLGBJ             1.0000    
 No IC found for species AGLYJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species APCSOJ in INIT_AERO_1; set to  1.00E-30
 No IC found for species ALVPO1I in INIT_AERO_1; set to  1.00E-30
 No IC found for species ASVPO1I in INIT_AERO_1; set to  1.00E-30
 No IC found for species ASVPO2I in INIT_AERO_1; set to  1.00E-30
 No IC found for species ALVPO1J in INIT_AERO_1; set to  1.00E-30
 No IC found for species ASVPO1J in INIT_AERO_1; set to  1.00E-30
 No IC found for species ASVPO2J in INIT_AERO_1; set to  1.00E-30
 No IC found for species ASVPO3J in INIT_AERO_1; set to  1.00E-30
 No IC found for species AIVPO1J in INIT_AERO_1; set to  1.00E-30
 No IC found for species APOCI in INIT_AERO_1; Look for         ALVOO1I
 No IC found for species ALVOO1I in INIT_AERO_1; set to  1.00E-30
 No IC found for species APOCI in INIT_AERO_1; Look for         ALVOO2I
 No IC found for species ALVOO2I in INIT_AERO_1; set to  1.00E-30
 No IC found for species ASVOO1I in INIT_AERO_1; set to  1.00E-30
 No IC found for species ASVOO2I in INIT_AERO_1; set to  1.00E-30
 No IC found for species APOCJ in INIT_AERO_1; Look for         ALVOO1J
 No IC found for species ALVOO1J in INIT_AERO_1; set to  1.00E-30
 No IC found for species APOCJ in INIT_AERO_1; Look for         ALVOO2J
 No IC found for species ALVOO2J in INIT_AERO_1; set to  1.00E-30
 No IC found for species ASVOO1J in INIT_AERO_1; set to  1.00E-30
 No IC found for species ASVOO2J in INIT_AERO_1; set to  1.00E-30
 No IC found for species ASVOO3J in INIT_AERO_1; set to  1.00E-30

 AE loaded into CGRID
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species ASO4 Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species ANO3 Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species ACL Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species ANH4 Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species ANA Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species AMG Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species AK Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species ACA Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species AFE Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species AMN Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species AH2O Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species AH3OP Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species ASOIL Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species ACORS Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species ASEACAT Not found in AE namelist
 
 
 >>--->> WARNING in subroutine Aero_Data on PE 000
 FATAL: Required Species ALVPO1 Not found in AE namelist
 
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD 
with errorcode 0.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

NOT FATAL: Optional Species APHGJ Not found in AE namelist.                    

FATAL Error(s) found in the AE namelist used. Check that 
this AE namelist contains the above required data as the file in 
the respository version of the mechanism: CB6R3_AE6_AQ


 *** ERROR ABORT in subroutine Aero_Data on PE 000       
 The FATAL errors found in namelist used. Check the log of exiting processor if more details are needed.
 Date&time specified as 0

I am running CCTM in serial currently, and the the AE namelist that CCTM is referencing (AE_cb6r3_ae6_aq.nml) has been copied into the $BLD directory. Nothing execpt input/output data paths have been chaged in run_cctm.csh. Any ideas?

Thanks,
Jeff

Havala.Pye · November 9, 2018, 3:31pm

Hi Jeff,
I’m not completely sure what the problem is, but it looks like your AE*.nml is not consistent with your build. Check your log file for the location of the AE*.nml and make sure it matches your build selections (aero6 in v5.2). Note namelists from one version of CMAQ (even if they are the same aero and chemistry version) are not compatible with another version of CMAQ.

The “No IC found for species…” are not fatal and can be overcome by including sufficient spinup time as aerosol have a short (~week) lifetime (see this paper by Hogrefe et al. for information on spinup time: https://doi.org/10.1016/j.atmosenv.2017.04.009)

Havala

Jsward · December 6, 2018, 8:37pm

Just for everyone who may encounter similar issues, my error was actually associated with the use of an older version of the GNU Fortran compiler installed on some compute nodes, so executables compiled on the machine’s head node could not correctly function on those compute nodes.

esm · April 13, 2019, 8:53am

Hi
I want to benchmark CMAQv5.21 on a system using pgi and mpif90. I just ran CCTM and it failed. Is it necessary to run bcon and icon,too?

lizadams · April 22, 2019, 3:11pm

Hi, I took a look at the Quickstart guide https://github.com/USEPA/CMAQ/blob/5.2.1/DOCS/User_Manual/CMAQ_OGD_quick_start.md, and it doesn’t say to run icon and bcon. I believe we provide the icon and bcon input files to CMAQv5.2.1 for the benchmark case. To help you with your error, please send the error message that you have received.

esm · April 23, 2019, 6:44pm

Hi Lizadams
Thank you for your answer.
Errors are:
mpirun -r ssh -np 8 /home/mechanic/CMAQ_yazgi/CMAQ_Compiled/CCTM/scripts/BLD_CCTM_v521_pgi/CCTM_v521.exe
[mpiexec@localhost.localdomain] match_arg (./utils/args/args.c:122): unrecognized argument r
[mpiexec@localhost.localdomain] HYDU_parse_array (./utils/args/args.c:140): argument matching returned error
[mpiexec@localhost.localdomain] parse_args (./ui/mpich/utils.c:1387): error parsing input array
[mpiexec@localhost.localdomain] HYD_uii_mpx_get_parameters (./ui/mpich/utils.c:1438): unable to parse user arguments

-disable-auto-cleanup            don't cleanup processes on error

I search the error in google. I find that the version of MPICH is old; but my version is 1.4. What do you think? Should I install the CMAQ again?

lizadams · April 23, 2019, 7:00pm

Please change the mpirun command to use
mpirun -np 8 /home/mechanic/CMAQ_yazgi/CMAQ_Compiled/CCTM/scripts/BLD_CCTM_v521_pgi/CCTM_v521.exe
The "-r ssh " portion of the command should be removed.

esm · April 23, 2019, 7:03pm

I tried it; but it didn’t run.

lizadams · April 23, 2019, 7:18pm

What is the error message that you are getting now?

esm · April 23, 2019, 7:19pm

I tried to run in serial way.but it didn’t run.run_cctm.csh (24.1 KB)
This is my CCTM. Could you check it, please?

lizadams · April 23, 2019, 7:21pm

Your run_cctm.csh looks fine. Please send the log file that you have obtained.
Please also try the mpirun command.

esm · April 23, 2019, 7:22pm

There isn’t any error. But I see some not match in log file.
I check the file paths, too.They were right.

esm · April 23, 2019, 7:32pm

New Text Document.txt (48.1 KB)
I can’t upload the log file, so I copy it in a text file.

lizadams · April 23, 2019, 7:45pm

Please verify that the mpirun command works using

mpirun -version

esm · April 23, 2019, 7:55pm

I must write:
time mpirun - 1.4 -np $NPROCS $BLD/$EXEC
Is that right?

lizadams · April 23, 2019, 7:56pm

time mpirun -np $NPROCS $BLD/$EXEC

esm · April 23, 2019, 7:58pm

so where I must write the version of mpirun?

lizadams · April 23, 2019, 7:59pm

To check the that the mpirun command works, you can either use it at the command line, or you can add it to your run_cctm.csh script at a line above the following command.

mpirun -version
time mpirun -np $NPROCS $BLD/$EXEC

esm · April 23, 2019, 8:03pm

Thank you so much. I’m not in the office now. I will try it and will tell you the result.

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