# Combine run Error
**URL:** https://forum.cmascenter.org/t/combine-run-error/1231
**Category:** Post-processing
**Created:** [January 9, 2020, 2:32pm UTC](https://forum.cmascenter.org/t/combine-run-error/1231 "2020-01-09T14:32:46Z")
**Posts on this page:** 9
**Page:** 1
### Author:  [@Nguyen\_Dong](https://forum.cmascenter.org/u/Nguyen_Dong)
#### Post date: [January 9, 2020, 2:32pm UTC](https://forum.cmascenter.org/t/combine-run-error/1231/1 "2020-01-09T14:32:46Z")
Hi all,
I’m trying to run the combine post-processor and come across the following error:
…
**WARNING** File does not exist:INFILE5
Value for GENSPEC: N returning FALSE
```
Value for IOAPI_CHECK_HEADERS not defined;returning default: FALSE
"OUTFILE" opened as OLD:READ-WRITE
File name "/home/hdong/CMAQv5.3/data/combine/COMBINE_ACONC_v53_gcc_14-01-2015_201501.nc"
File type GRDDED3
Execution ID "????????????????"
Grid name "HN-01-2015"
Dimensions: 24 rows, 27 cols, 1 lays, 134 vbles
NetCDF ID: 327680 opened as READWRITE
Starting date and time 2015014:130000 (13:00:00 Jan. 14, 2015)
Timestep 010000 (1:00:00 hh:mm:ss)
Maximum current record number 0
```
Processing starting at: 2015014 130000
ending at: 2015014 220000
Copying Variables at time:2015014:130000
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0x7f584601cef7 in ???
#1 0x7f584601c12d in ???
#2 0x7f584550f4af in ???
#3 0x7f584550f428 in ???
#4 0x7f5845511029 in ???
#5 0x7f58455517e9 in ???
#6 0x7f584555a379 in ???
#7 0x7f584555e53b in ???
#8 0x416336 in ???
#9 0x416f45 in ???
#10 0x41a1ed in ???
#11 0x41e96e in ???
#12 0x4035ac in ???
#13 0x7f58454fa82f in ???
#14 0x4035d8 in ???
#15 0xffffffffffffffff in ???
Abort (core dumped)
I don’t know why it’s trying to open INFILE5 when there should be only 4 input files. And it also should be able to create the OUTFILE, in COMBINE\_DEP\_v53\_gcc\_14-01-2015\_201501 file have data, but in COMBINE\_ACONC\_v53\_gcc\_14-01-2015\_201501.nc file have not data. Any advice?
And here are my scripts and log files.
Thanks!
[run\_combine.csh](https://forum.cmascenter.org/uploads/short-url/8AIrRO2FBWIorJLVt6hdogP3zsf.csh) (7.3 KB)
[combine\_v53.log.txt](https://forum.cmascenter.org/uploads/short-url/y57zvtILgtWGFGGjNDQM1h2c471.txt) (64.2 KB)
---
### Author:  [@hogrefe.christian](https://forum.cmascenter.org/u/hogrefe.christian)
#### Post date: [January 9, 2020, 2:59pm UTC](https://forum.cmascenter.org/t/combine-run-error/1231/2 "2020-01-09T14:59:40Z")
The warning about the missing INFILE5 is just that, a warning, and doesn’t cause the problem you are reporting. The executable doesn’t know how many INFILEs there are, so it just tries to open them sequentially until it encounters one that is undefined (note that the successful ‘combine’ run for deposition also has this warning, but since INFILE4 was explicitly defined as blank in the script, the warning looks a bit different than when running ‘combine’ for aconc).
It’s hard to tell what’s causing the crash when running for ‘aconc’, but it may be a memory issue. My two suggestions are to 1) compile ‘combine’ in debug mode to see if there any more specific error messages, and 2) edit CMAQ\_HOME/POST/combine/scripts/spec\_def\_files/SpecDef\_${MECH}.txt to create a test version with just a few species instead of the many species currently defined and see if this helps.
---
### Author:  [@lizadams](https://forum.cmascenter.org/u/lizadams)
#### Post date: [January 9, 2020, 3:40pm UTC](https://forum.cmascenter.org/t/combine-run-error/1231/3 "2020-01-09T15:40:05Z")
Your run script performs two different combine runs. The first to create an output file called COMBINE\_ACONC\* , and the second to create the output file called COMBINE\_DEP\* . The first step is failing, while the second succeeds.
According to your log file, you have an output file that already exists.
Can you try removing that and rerunning only the first part of your run script.
```
"OUTFILE" opened as **OLD:READ-WRITE**
File name "/home/hdong/CMAQv5.3/data/combine/COMBINE_ACONC_v53_gcc_14-01-2015_201501.nc"
File type GRDDED3
Execution ID "????????????????"
Grid name "HN-01-2015"
Dimensions: 24 rows, 27 cols, 1 lays, 134 vbles
NetCDF ID: 327680 opened as READWRITE
Starting date and time 2015014:130000 (13:00:00 Jan. 14, 2015)
Timestep 010000 (1:00:00 hh:mm:ss)
Maximum current record number 0
```
Processing starting at: 2015014 130000
ending at: 2015014 220000
Copying Variables at time:2015014:130000
Program received signal SIGABRT: Process abort signal.
---
### Author:  [@Nguyen\_Dong](https://forum.cmascenter.org/u/Nguyen_Dong)
#### Post date: [January 9, 2020, 3:53pm UTC](https://forum.cmascenter.org/t/combine-run-error/1231/4 "2020-01-09T15:53:53Z")
Thank you for replying but I use a Dell Precision 7510 15.6-inch Full HD Core i7 6820HQ laptop / 32GB RAM / 1TB SSD / NVIDIA so I think it works well for this.
---
### Author:  [@Nguyen\_Dong](https://forum.cmascenter.org/u/Nguyen_Dong)
#### Post date: [January 9, 2020, 3:56pm UTC](https://forum.cmascenter.org/t/combine-run-error/1231/5 "2020-01-09T15:56:02Z")
Thanks for answering.
I have tried following your instructions but it did not solve the problem.
Do you have any other suggestions?
Sincere thanks.
---
### Author:  [@lizadams](https://forum.cmascenter.org/u/lizadams)
#### Post date: [January 9, 2020, 4:44pm UTC](https://forum.cmascenter.org/t/combine-run-error/1231/6 "2020-01-09T16:44:09Z")
Assuming that the Species Definition file: SpecDef\_cb6r3\_ae7\_aq.txt is OK
The first variable that it tries to write out is AIR\_DENS, which should be coming from the METCRO3D file.
AIR\_DENS ,kg m-3 ,DENS[2]
/ File [2]: METCRO3D file
I noticed that you have a different Grid name in your log file between INFILE1 and INFILE2.
```
"INFILE1" opened as OLD:READ-ONLY
File name "/home/hdong/CMAQv5.3/data/cctm/14-01-2015/CCTM_ACONC_14-01-2015_20150114.nc"
File type GRDDED3
Execution ID "CMAQ_CCTMv53_hdong_20200107_162831_453815532"
Grid name "HN-01-2015"
Dimensions: 24 rows, 27 cols, 1 lays, 226 vbles
NetCDF ID: 65536 opened as READONLY
Starting date and time 2015014:130000 (13:00:00 Jan. 14, 2015)
Timestep 010000 (1:00:00 hh:mm:ss)
Maximum current record number 10
"INFILE2" opened as OLD:READ-ONLY
File name "/home/hdong/CMAQv5.3/data/mcip/14-01-2015/METCRO3D_14-01-2015.nc"
File type GRDDED3
Execution ID "mcip"
Grid name "HN-01-2015_CROSS"
Dimensions: 24 rows, 27 cols, 32 lays, 18 vbles
NetCDF ID: 131072 opened as READONLY
Starting date and time 2015014:130000 (13:00:00 Jan. 14, 2015)
Timestep 010000 (1:00:00 hh:mm:ss)
Maximum current record number 12
```
I thought that it may cause a problem, but perhaps not. Can you use ncdump -h to determine if DENS is available in the METCRO3D\_14-01-2015.nc file
---
### Author:  [@Nguyen\_Dong](https://forum.cmascenter.org/u/Nguyen_Dong)
#### Post date: [January 9, 2020, 4:53pm UTC](https://forum.cmascenter.org/t/combine-run-error/1231/7 "2020-01-09T16:53:54Z")
Thanks lizadams
But the file creation COMBINE\_DEP \* does not matter though its source files also have such Grid names.
---
### Author:  [@lizadams](https://forum.cmascenter.org/u/lizadams)
#### Post date: [January 9, 2020, 5:51pm UTC](https://forum.cmascenter.org/t/combine-run-error/1231/8 "2020-01-09T17:51:41Z")
1. First, recompile the combine executable to use debug mode
i. make clean
ii. setenv DEBUG true
iii. make
iv. rerun the combine script and see if you get a traceback to tell us what is causing the abort
2. Then please verify that your species definition file is not corrupted.
i. compare your species def to the one in the repo using the diff command: CMAQ\_REPO/CCTM/src/MECHS/cb6r3\_ae7\_aq/SpecDef\_cb6r3\_ae7\_aq.txt
3. Please also use ncdump -h to verify that the variable DENS is available in the METCRO3D\_14-01-2015.nc file.
---
### Author:  [@Nguyen\_Dong](https://forum.cmascenter.org/u/Nguyen_Dong)
#### Post date: [January 10, 2020, 2:46pm UTC](https://forum.cmascenter.org/t/combine-run-error/1231/9 "2020-01-10T14:46:15Z")
Thank you for your comments.
I found the error: on the third line “#layer 1” in the SpecDef\_cb6r3\_ae7\_aq.txt file I added an “!” before “#”.
Thank you once again.