# CMAQv5.3 2-day benchmark index error
**URL:** https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973
**Category:** Run Time Errors and Issues
**Created:** [September 25, 2019, 8:08pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973 "2019-09-25T20:08:30Z")
**Posts on this page:** 18
**Page:** 1
### Author:  [@jdeast2](https://forum.cmascenter.org/u/jdeast2)
#### Post date: [September 25, 2019, 8:08pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/1 "2019-09-25T20:08:30Z")
Hi all,
I am running the 2-day benchmark for CMAQv5.3. The 1st day successfully runs, but the 2nd day fails almost immediately with an indexing error “NCVGT: : NetCDF: Index exceeds dimension bound”
The last statement in all the CTM log files is:
> ```
> "E2C_CHEM_YEST" opened as OLD:READ-ONLY
> File name "/share/fgarcia4/jdeast2/cmaq-5.3-intel2017-BENCH/CMAQ_REPO/data/2016_12SE1//land/epic_festc1.4_20180516/2016_US1_time20160701_bench.nc"
> File type GRDDED3
> Execution ID "????????????????"
> Grid name "SE53BENCH"
> Dimensions: 80 rows, 100 cols, 42 lays, 41 vbles
> NetCDF ID: 2555904 opened as READONLY
> Starting date and time 2016183:000000 (0:00:00 July 1, 2016)
> Timestep 240000 (24:00:00 hh:mm:ss)
> Maximum current record number 1
> Checking header data for file: E2C_CHEM_YEST
> Inconsistent values for NLAYS: 42 versus 35
>
> ```
This seems as if the E2C\_CHEM\_YEST file has mismatching dimensions, but the file for day 1 has the same dimensions and there is no error in day 1. The inconsistent NLAYS does not seem to cause the model to fail when it happens in other files.
Any help solving this error is appreciated! My run script is attached. There are only minor changes to paths from the run script packaged with the benchmark data.
Thanks,
James
[run\_cctm\_Bench\_2016\_12SE1.csh](https://forum.cmascenter.org/uploads/short-url/w83ZZM5bEBPEQKdCNVCNWgEMih5.csh) (31.8 KB)
---
### Author:  [@zyj.jess](https://forum.cmascenter.org/u/zyj.jess)
#### Post date: [September 26, 2019, 1:38pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/2 "2019-09-26T13:38:58Z")
Hi, James;
I encountered with this NCVGT error many times. The scenarios I was in when I saw this error message was the dimensions of my inputs file were not matching each other. Especially, I had this error when my initial condition or boundary condition had a different dimension such as time step. It could be a hint for you to check the time step of this soil file or other input files. As far as I know, once the dimension issue is fixed, you should have no problem at this point.
Hope this helps!
Best;
Yijia
---
### Author:  [@lizadams](https://forum.cmascenter.org/u/lizadams)
#### Post date: [September 26, 2019, 4:25pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/3 "2019-09-26T16:25:18Z")
Please share a copy of your CTM\_LOG\_000\* file.
It should be located in the following directory:
data/output\_CCTM\_v53\_gcc\_Bench\_2016\_12SE1/LOGS
---
### Author:  [@jdeast2](https://forum.cmascenter.org/u/jdeast2)
#### Post date: [September 26, 2019, 5:40pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/4 "2019-09-26T17:40:08Z")
Thank you! In this case, the dimensions of the input boundary and initial conditions files match (80x100x35). Besides the inconsistent NLAYS, all input files appear to have 80x100 except DOT met files and point emissions
---
### Author:  [@jdeast2](https://forum.cmascenter.org/u/jdeast2)
#### Post date: [September 26, 2019, 5:43pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/5 "2019-09-26T17:43:43Z")
Here is the CTM\_LOG\_000 file:
Thank you!
[CTM\_LOG\_000.v53\_intel2017\_Bench\_2016\_12SE1\_20160702.txt](https://forum.cmascenter.org/uploads/short-url/zfzxZQEisKS8At7WYgU2LsPEwVl.txt) (49.6 KB)
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### Author:  [@lizadams](https://forum.cmascenter.org/u/lizadams)
#### Post date: [September 26, 2019, 6:18pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/6 "2019-09-26T18:18:51Z")
Can you use the following command to search for an ERROR statement in all of the log files:
grep -i ERROR CTM\_LOG\_\*
Is there an error message in any of the other CTM\_LOG files?
The warning that you are seeing would not cause the model to fail.
---
### Author:  [@jdeast2](https://forum.cmascenter.org/u/jdeast2)
#### Post date: [September 30, 2019, 12:08pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/7 "2019-09-30T12:08:30Z")
Searching with that command shows no error messages in any of the log files.
Additionally, here’s the output created by the system job scheduler that contains the actual error and some other output not contained in the LOG files.
Should any changes to the benchmark run script provided with the CMAQ distribution have to be made to run the simulation? I had to make a few changes.
[out.cmq53.761790.txt](https://forum.cmascenter.org/uploads/short-url/xCHRxiLQRdPFXapD8B5sB7TOFbG.txt) (238.9 KB)
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### Author:  [@lizadams](https://forum.cmascenter.org/u/lizadams)
#### Post date: [September 30, 2019, 1:21pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/8 "2019-09-30T13:21:53Z")
Hi James,
You should not have a problem running the benchmark version with the scripts provided.
However, it looks like you are using an older version of the I/O API library.
Please try downloading and using the latest version. Here is the information on the version that I am using:
```
ioapi-3.2: $Id: init3.F90 120 2019-06-21 14:18:20Z coats $
Version with PARMS3.EXT/PARAMETER::MXVARS3= 2048
netCDF version 4.7.0 of Sep 16 2019 15:07:57 $
```
I followed these instructions to download and install.
>
---
### Author:  [@jdeast2](https://forum.cmascenter.org/u/jdeast2)
#### Post date: [September 30, 2019, 7:16pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/9 "2019-09-30T19:16:35Z")
Hi Liz,
I’m using IOAPI-3.2, which matches yours. Where do you see that I have an old version? Perhaps something is linked incorrectly for me.
I’ve tried several things but still encountering the same error:
> NCVGT: : NetCDF: Index exceeds dimension bound
Is it possible that it is related to time steps in the simulation?
Thanks,
James
---
### Author:  [@lizadams](https://forum.cmascenter.org/u/lizadams)
#### Post date: [September 30, 2019, 7:30pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/10 "2019-09-30T19:30:25Z")
Hi James,
You are correct that we have the same Models-3 I/O API version number, but the dates are different.
In your out.cmq53.761790.txt file is the following output:
```auto
ioapi-3.2: $Id: init3.F90 98 2018-04-05 14:35:07Z coats $
netCDF version 4.6.1 of Nov 12 2018 11:27:53 $
```
---
### Author:  [@jdeast2](https://forum.cmascenter.org/u/jdeast2)
#### Post date: [October 1, 2019, 6:06pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/11 "2019-10-01T18:06:35Z")
Hi Liz,
I installed the most recent version of ioapi available and both days ran successfully.
The version used now matches yours:
> ioapi-3.2: Id: init3.F90 120 2019-06-21 14:18:20Z coats
Thank you for your help!
---
### Author:  [@thayna.gomes](https://forum.cmascenter.org/u/thayna.gomes)
#### Post date: [December 4, 2019, 1:07am UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/12 "2019-12-04T01:07:23Z")
Dear @lizadams
I’m also having problem running CMAQ v5.3. However, I’m did not find any message that may point to the error.
Do you think that if we update I/O API library it would run succesfully?
Please find attached run script and log files.
If you find any possible mistake, please let me know. I would appreciate the support.
Thank you in advance!
[run\_cctm\_2010\_RMGV.csh](https://forum.cmascenter.org/uploads/short-url/kINzTKUI4iLo2Hlyng5vISl1BpC.csh) (34.5 KB) [CTM\_LOG\_000.v53\_intel\_RMGV\_20100723.txt](https://forum.cmascenter.org/uploads/short-url/9XMUwzlIfBJQuS4Z4xOz83NAtxr.txt) (47.8 KB) [CTM\_LOG\_001.v53\_intel\_RMGV\_20100723.txt](https://forum.cmascenter.org/uploads/short-url/E3AoHrpsuh5W9VqPPwMzGkhseK.txt) (34.7 KB) [CTM\_LOG\_002.v53\_intel\_RMGV\_20100723.txt](https://forum.cmascenter.org/uploads/short-url/suGHhh5Mcf0KP7uaShz0kNMJNtq.txt) (34.7 KB) [CTM\_LOG\_003.v53\_intel\_RMGV\_20100723.txt](https://forum.cmascenter.org/uploads/short-url/w5wk3jq5mnBRlatHvxRmtELW1rF.txt) (34.7 KB) [CTM\_LOG\_004.v53\_intel\_RMGV\_20100723.txt](https://forum.cmascenter.org/uploads/short-url/onvByPEQP8fKHHSBCT4J441Pvl1.txt) (34.7 KB) [CTM\_LOG\_005.v53\_intel\_RMGV\_20100723.txt](https://forum.cmascenter.org/uploads/short-url/cokIO5cAVw8nOu2R9UcVB2lDWWh.txt) (34.7 KB) [CTM\_LOG\_006.v53\_intel\_RMGV\_20100723.txt](https://forum.cmascenter.org/uploads/short-url/uWg83f1wXPOPleEPMLPbdnqLvIO.txt) (34.7 KB) [CTM\_LOG\_007.v53\_intel\_RMGV\_20100723.txt](https://forum.cmascenter.org/uploads/short-url/hnGSanSRv9CAjIOXBxitb3oTeh8.txt) (34.7 KB) [CTM\_LOG\_008.v53\_intel\_RMGV\_20100723.txt](https://forum.cmascenter.org/uploads/short-url/yrDiedyvfzLgF1HKQi6dl8tamMT.txt) (34.7 KB) [log\_run\_cctm\_2010\_RMGV.txt](https://forum.cmascenter.org/uploads/short-url/pQJKtHS9uH1RVWXHjVUB5d77dAd.txt) (22.2 KB)
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### Author:  [@maplewind](https://forum.cmascenter.org/u/maplewind)
#### Post date: [December 4, 2019, 2:35am UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/13 "2019-12-04T02:35:33Z")
Hi Liz,
Is it necessary to run CMAQ v5.3 with using IOAPI-3.2.
When I ran CMAQ v5.3 with IOAPI-3.1 ,there are no distinct errors in log files.
Thanks！
---
### Author:  [@thayna.gomes](https://forum.cmascenter.org/u/thayna.gomes)
#### Post date: [December 4, 2019, 7:47pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/14 "2019-12-04T19:47:06Z")
What about version of I/O API-3.2?
I’m running with:
ioapi-3.2: Id: init3.F90 3 2017-04-15 20:19:16Z coats
netCDF version 4.4.1.1 of Aug 7 2017 18:04:11 $
I’m having trouble as commented in my post.
> [@CMAQv5.3 2-day benchmark index error](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/12):
>
> Dear @lizadams I’m also having problem running CMAQ v5.3. However, I’m did not find any message that may point to the error. Do you think that if we update I/O API library it would run succesfully? Please find attached run script and log files. If you find any possible mistake, please let me know. I would appreciate the support. Thank you in advance! [run\_cctm\_2010\_RMGV.csh](https://forum.cmascenter.org/uploads/short-url/kINzTKUI4iLo2Hlyng5vISl1BpC.csh) (34.5 KB) [CTM\_LOG\_000.v53\_intel\_RMGV\_20100723.txt](https://forum.cmascenter.org/uploads/short-url/9XMUwzlIfBJQuS4Z4xOz83NAtxr.txt) (47.8 KB) [CTM\_LOG\_001.v53\_intel\_RMGV\_20100723.txt](https://forum.cmascenter.org/uploads/short-url/E3AoHrpsuh5W9VqPPwMzGkhseK.txt) (34.7 KB) [CTM\_LOG\_…](https://forum.cmascenter.org/uploads/short-url/suGHhh5Mcf0KP7uaShz0kNMJNtq.txt)
Thank you!
---
### Author:  [@cjcoats](https://forum.cmascenter.org/u/cjcoats)
#### Post date: [December 4, 2019, 8:35pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/15 "2019-12-04T20:35:22Z")
It is conceivable that you can get rid of this by getting rid of all the executable, object, module, and library files, and then re-building from scratch.
The October 16 I/O API release increased the maximum-files parameter MXFILE3 from 64 to 256 at the request of EPA. This increase should have been transparent to any application which does not include/use I/O API-internal/private data structures in STATE3.EXT – doing so is forbidden, but CMAQ’s “pario” uses these anyway. This may be the cause of the problem.
---
### Author:  [@lizadams](https://forum.cmascenter.org/u/lizadams)
#### Post date: [December 4, 2019, 9:45pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/16 "2019-12-04T21:45:36Z")
I am not familiar with the error that is reported in your log\_run\_cctm\_2010\_RMGV.txt
"forrtl: severe (27): too many records in I/O statement, unit -5, file Internal Formatted "
Can you change the run script to set the CLOBBER\_DATA to true and try running again?
```auto
#> Keep or Delete Existing Output Files
set CLOBBER_DATA = TRUE
```
---
### Author:  [@thayna.gomes](https://forum.cmascenter.org/u/thayna.gomes)
#### Post date: [December 5, 2019, 11:57am UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/17 "2019-12-05T11:57:22Z")
Dear @lizadams
Thank you for the suggestion, but I am still having the same problem.
Do you any other suggestion?
I really appreciate the support!
[cmaq\_log\_file.txt](https://forum.cmascenter.org/uploads/short-url/xvUY42x22SFASmJACi3iZwXfLTv.txt) (22.3 KB) [run\_cctm\_2010\_RMGV.csh](https://forum.cmascenter.org/uploads/short-url/w7i92eIGl6HCAl3cWNqIzvM7nKH.csh) (33.7 KB) [CTM\_LOG\_000.txt](https://forum.cmascenter.org/uploads/short-url/8Xgrf2ahi7bvRJ6dMBqFkVZECd1.txt) (42.6 KB)
---
### Author:  [@cjcoats](https://forum.cmascenter.org/u/cjcoats)
#### Post date: [December 5, 2019, 1:37pm UTC](https://forum.cmascenter.org/t/cmaqv5-3-2-day-benchmark-index-error/973/18 "2019-12-05T13:37:57Z")
Re-compile the code with “-traceback” and that will at least indicate the source-file and line at which the error occurs. I would not be surprised if the error happens due to a bad format during the construction of an error-message for the “real” error; if so, then fixing that format might then help to get the real error-message out to the log, and we can go from there (two-stage process, sorry).