Hi, I recently installed CMAQ 5.3.2 and trying to run test cases. The base case runs successfully but when I try to run ISAM case, it stops with an error, looking at the log files, the end lines are:
*** ERROR ABORT in subroutine SA_IOLIST on PE 002
Error Opening SA_IO_LIST file
PM3EXIT: date&time specified as 0
Date&time specified as 0
Just wondering if anyone can give some insight on resolving this error. Thanks in advance
Please take a look at the following tutorial.
I have followed line by line these instructions while running the ISAM. Could you please point out which step I might be doing wrong?
Did you change anything in the CMAQ-ISAM tag definition control file or are you using the default version? Please attach your version of the isam_control.txt.
I have not changed anything in the control file. When I try to attach it says new users cannot upload attachments. I am copying the contents of the isam_control.txt below:
!!! CMAQ-ISAM tag definition control file
!!! (lines begining with !!! - three exclamation marks - are ignored by the text parser)!!!
!!!
!!! Example file provided with CMAQ v5.3.2 release
!!! 26 July 2020: Sergey L. Napelenok
!!!
!!!
!!! The “TAG CLASSES” line defines the tag classes to track for the simulation. Species in NITRATE and VOC classes depend on the
!!! the chemical mechanism used. The below definitions apply for the cb6r3_ae7_aq mechanism. These species will be tracked for
!!! each user-defiend source.
!!! Choose any/all from the list of nine: SULFATE, NITRATE, AMMONIUM, EC, OC, VOC, PM25_IONS, OZONE, CHLORINE
!!! SULFATE - ASO4J, ASO4I, SO2, SULF, SULRXN
!!! NITRATE - ANO3J, ANO3I, HNO3, NO, NO2, NO3, HONO, N2O5, PNA, PAN, PANX, NTR1, NTR2, INTR, CLNO2, CLNO3
!!! AMMONIUM - ANH4J, ANH4I, NH3
!!! EC - AECJ, AECI
!!! OC - APOCI, APOCJ, APNCOMI, APNCOMJ
!!! VOC - Various species depending on mechanism. Now includes CO. (see CCTM/src/isam/SA_DEFN.F for complete list)
!!! PM25_IONS - ANAI, ANAJ, AMGJ, AKJ, ACAJ, AFEJ, AALJ, ASIJ, ATIJ, AMNJ, AOTHRI, AOTHRJ
!!! OZONE - O3, all NITRATE species, and all VOC species
!!! CHLORINE - ACLI, ACLJ, HCL
TAG CLASSES |SULFATE, OZONE
!!! The following are source definition text blocks in the format. Provide a 3-line block for each source you want to track.
!!! Do not assign the same source of mass in more than 1 source definition block.
!!! TAG NAME |Three character text string (unique to each source definition)
!!! REGION(S) |Keyword EVERYWHERE or variable names from the region file (multiple regions need to be comma delimited)
!!! FILENAME(S) |Emissions labels (multiple labels need to be comma delimited)
TAG NAME |GAE
REGION(S) |GA
EMIS STREAM(S) |PT_EGU
TAG NAME |GAF
REGION(S) |GA
EMIS STREAM(S) |PT_FIRES
TAG NAME |NCE
REGION(S) |NC
EMIS STREAM(S) |PT_EGU
TAG NAME |NCF
REGION(S) |NC
EMIS STREAM(S) |PT_FIRES
ENDLIST eof
In the log script where you found that " ERROR ABORT " message, search for other instances of the character string “SA_IO_LIST”. One of these instances should be a path/filename of the file that it is trying to open. This is defined in the runscript. Make sure that it is defined correctly in the runscript and that the file it is looking for exists.
Sergey
Thanks @sergey , I resolved that issue. But currently stuck with the program abruptly ends after two iterations, here is the message on the screen. The log files do not say any error, but gives a warning that ISAM species not found in CHEMISTRY_SPC.I would have attached the log file but as a new user I cannot (not sure how long I will stay as new user).
VDIFF completed... 4.1 seconds
COUPLE completed... 0.1 seconds
HADV completed... 1.8 seconds
ZADV completed... 0.7 seconds
HDIFF completed... 0.2 seconds
DECOUPLE completed... 0.1 seconds
PHOT completed... 2.0 seconds
CLDPROC completed... 0.4 seconds
CHEM completed... 13.9 seconds
AERO completed... 11.6 seconds
Master Time Step
Processing completed... 35.0 seconds
Processing Day/Time [YYYYDDD:HHMMSS]: 2016183:000500
Which is Equivalent to (UTC): 0:05:00 Friday, July 1, 2016
Time-Step Length (HHMMSS): 000500
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
Command exited with non-zero status 9
real 59.44
user 167.19
sys 6.48
** Runscript Detected an Error: CGRID file was not written. **
** This indicates that CMAQ was interrupted or an issue **
** exists with writing output. The runscript will now **
** abort rather than proceeding to subsequent days. **
*************************************************************CTM_LOG_000.v532_ISAM_gcc_Bench_2016_12SE1_20160701.txt (199.7 KB) CTM_LOG_001.v532_ISAM_gcc_Bench_2016_12SE1_20160701.txt (182.7 KB) CTM_LOG_002.v532_ISAM_gcc_Bench_2016_12SE1_20160701.txt (181.2 KB) CTM_LOG_003.v532_ISAM_gcc_Bench_2016_12SE1_20160701.txt (182.7 KB)
I’ve upgraded you to a “regular user”, let me know if you can upload files now.
Yes I am able to upload the files. Thanks @lizadams
@sergey , I am still stuck at this, do you have any suggestion to resolve this?
Hi SharMM,
Sorry for the delayed response, but I don’t see any error messages in the log files you provided aside from the MPI error message you provide in the email. The warning about ASO4I is not causing any problem. That is the correct behavior. It probably shouldn’t even be a warning at all. This is what we want.
This EXIT CODE: 9 thing could mean that something is wrong with the code, but I don’t see that here. It could also mean that one or more of the nodes just died somehow, got rebooted, ran out of memory, or ran out of time in the job scheduler or something like that on your machine.
I would try to see if you just need more or different hardware resources for your job, or see if you can make the job smaller on the same resources.
Sergey
Hello, I have met the same problem:
*** ERROR ABORT in subroutine SA_IOLIST on PE 002
Error Opening SA_IO_LIST file
PM3EXIT: date&time specified as 0
Date&time specified as 0
Just wondering how did you solve this problem? Thanks a lot.
This is a duplicate post. See the response at this issue: Error in running CMAQ-ISAM 5.3.2, error opening SA_IO_LIST file