# How to run CMAQ-ISAM
**URL:** https://forum.cmascenter.org/t/how-to-run-cmaq-isam/1606
**Category:** CMAQ-ISAM
**Created:** [June 29, 2020, 7:32pm UTC](https://forum.cmascenter.org/t/how-to-run-cmaq-isam/1606 "2020-06-29T19:32:52Z")
**Posts on this page:** 11
**Page:** 1
### Author:  [@ykaore](https://forum.cmascenter.org/u/ykaore)
#### Post date: [June 29, 2020, 7:32pm UTC](https://forum.cmascenter.org/t/how-to-run-cmaq-isam/1606/1 "2020-06-29T19:32:52Z")
Hi all,
I am trying to run the CMAQ-ISAM, however for some reason that I cannot figure out yet, the files relate to the ISAM mode are not generated (CCTM\_SA\_ACONC, CCTM\_SA\_CONC). I am attaching the run script, the isam control file and the log (which ended before the run finished since I am doing several tests till I get what I want to). The CMAQ generated the CCTM\_ACONC, CCTM\_CONC, CCTM\_APMDIAG and CCTM\_PMDIAG netcdf files perfectly.
[geos\_cctm.csh](https://forum.cmascenter.org/uploads/short-url/vu6XBpDbbVViAfqXccks014qtIJ.csh) (34.2 KB) [isam\_control.txt](https://forum.cmascenter.org/uploads/short-url/oZBdHMqktqRCGC6HOYHN6dE1Gc4.txt) (1.6 KB)
[log.txt](https://forum.cmascenter.org/uploads/short-url/rq4znLyJgximUsKBK2goUchbT8A.txt) (152.4 KB)
I am also attaching the bldit\_cctm.csh file and its log, to show how I compiled the CMAQ-ISAM (I followed the User Manual which says that I have to uncomment the ISAM\_CCTM variable)
[bldit\_cctm.csh](https://forum.cmascenter.org/uploads/short-url/qP5OILP91J4CJRZRXqoB6GVeGba.csh) (28.6 KB)
[build\_log.txt](https://forum.cmascenter.org/uploads/short-url/60wqweSmROMxdEEnC1Tm0vfYyqZ.txt) (139.6 KB)
Thank you already for the help
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### Author:  [@fliu](https://forum.cmascenter.org/u/fliu)
#### Post date: [June 29, 2020, 11:19pm UTC](https://forum.cmascenter.org/t/how-to-run-cmaq-isam/1606/2 "2020-06-29T23:19:36Z")
Hello ykaore,
Please try to use the updated ISAM control file attached. You may check your emission control file otherwise. I hope this helps.
[isam\_control.txt](https://forum.cmascenter.org/uploads/short-url/irF8W8jMRBNS29e5vZoIzxkKMxe.txt) (2.7 KB)
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### Author:  [@sergey](https://forum.cmascenter.org/u/sergey)
#### Post date: [June 30, 2020, 12:12pm UTC](https://forum.cmascenter.org/t/how-to-run-cmaq-isam/1606/3 "2020-06-30T12:12:09Z")
Your build script does looks correct.
As far as your control file, it will not work the way you have it. You have to define the tags one at a time and there can only be 1 name in the TAG NAME field. For example:
TAG NAME |GR1
TAG CLASSES |SULFATE, OZONE, NITRATE, PM25\_IONS
REGION(S) |EVERYWHERE
EMIS STREAM(S) |AGRICULTURE
Fliu was on the right track, except this user created identical “EMIS STREAM(S)” calls for each tag, which would oversubscribe the emissions and crash. You can assign multiple emissions to one TAG NAME, and that will calculate the cumulative impact. You can’t assign the same mass in multiple places.
Note that we are in the processes of releasing a major update for ISAM that will drastically change OZONE predictions in the next few weeks. The update is finished, its just going through review. So, while it will be helpful to use the old code to resolve issues like you are having, I would wait for the new release before interpreting the results. The problem we are solving with the update is documented in the “Known Issues” in the repository. The update also includes some error checking for the control file, which should give you some more clues in situations like yours.
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### Author:  [@ykaore](https://forum.cmascenter.org/u/ykaore)
#### Post date: [June 30, 2020, 2:42pm UTC](https://forum.cmascenter.org/t/how-to-run-cmaq-isam/1606/4 "2020-06-30T14:42:52Z")
Thank you Fliu and Sergey for your help.
I did what both suggested, and nothing changed. I still dont get the output files from the ISAM. I am using the default emission control file (the one that comes with the installation of the mechanism cb6r3\_ae7\_aq[EmissCtrl\_cb6r3\_ae7\_aq.txt](https://forum.cmascenter.org/uploads/short-url/hjrYXvrO6OlN1NtJDfZotXee6f7.txt) (31.3 KB) )
Rearding the updating, I’ll keep an eye on it.
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### Author:  [@ykaore](https://forum.cmascenter.org/u/ykaore)
#### Post date: [July 16, 2020, 1:34pm UTC](https://forum.cmascenter.org/t/how-to-run-cmaq-isam/1606/5 "2020-07-16T13:34:44Z")
Dear @sergey,
I am sending this message just wondering about whether the release of the new CMAQ-ISAM is coming or not. Do you have any news about it?
Thank you very much.
Yasmin
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### Author:  [@sergey](https://forum.cmascenter.org/u/sergey)
#### Post date: [July 20, 2020, 7:48pm UTC](https://forum.cmascenter.org/t/how-to-run-cmaq-isam/1606/6 "2020-07-20T19:48:34Z")
Hi Yasmin,
I hope you worked out your earlier issue.
We are in the final testing stages of releasing the major update to ISAM. I was hoping it would be out by now, but we kept running into bugs. There were some drastic changes to the chemistry, which makes for much better results. I believe that at this point, we have worked out the bugs. We should be forwarding it to CMAS in a week or two, and they will run their own benchmark test before releasing.
Sergey
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### Author:  [@Catalyst2682](https://forum.cmascenter.org/u/Catalyst2682)
#### Post date: [December 6, 2020, 12:07pm UTC](https://forum.cmascenter.org/t/how-to-run-cmaq-isam/1606/7 "2020-12-06T12:07:03Z")
Dear @sergey, @fliu,
I have two isam\_control.txt files, I don’t know which one is correct. Below are the two:
Format 1:
TAG NAME |GR1
TAG CLASSES |PM25\_IONS
REGION(S) |EVERYWHERE
EMIS STREAM(S) |GRIDDED\_EMIS
TAG NAME |GR1
TAG CLASSES |OZONE
REGION(S) |EVERYWHERE
EMIS STREAM(S) |GRIDDED\_EMIS
TAG NAME |GR1
TAG CLASSES |SULFATE
REGION(S) |EVERYWHERE
EMIS STREAM(S) |GRIDDED\_EMIS
TAG NAME |GR1
TAG CLASSES |NITRATE
REGION(S) |EVERYWHERE
EMIS STREAM(S) |GRIDDED\_EMIS
Format 2:
TAG NAME |GR1
TAG CLASSES |SULFATE, OZONE, NITRATE, PM25\_IONS
REGION(S) |EVERYWHERE
EMIS STREAM(S) |GRIDDED\_EMIS
Thanks in anticipation.
Catalyst
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### Author:  [@sergey](https://forum.cmascenter.org/u/sergey)
#### Post date: [December 8, 2020, 10:44pm UTC](https://forum.cmascenter.org/t/how-to-run-cmaq-isam/1606/8 "2020-12-08T22:44:13Z")
This thread was supporting the old ISAM version. New new release (October 2020) slightly changed the control file. Check the documentation provided with the release, but the input file supported by the model is something like:
TAG CLASSES |SULFATE, OZONE, NITRATE, PM25\_IONS
TAG NAME |GR1
REGION(S) |EVERYWHERE
EMIS STREAM(S) |GRIDDED\_EMIS
You specific the TAG CLASSES only once at the top. All of the TAG NAMEs will use the same TAG CLASSES in a given simulation.
Sergey
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### Author:  [@Catalyst2682](https://forum.cmascenter.org/u/Catalyst2682)
#### Post date: [December 8, 2020, 10:58pm UTC](https://forum.cmascenter.org/t/how-to-run-cmaq-isam/1606/9 "2020-12-08T22:58:08Z")
Dear @sergey,
Yes, I have modified my control file to this format. The problem I am facing now has to do with UNITS while running the CCTM. Let me mention you in the thread again for possible solution.
Thanks
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### Author:  [@ykaore](https://forum.cmascenter.org/u/ykaore)
#### Post date: [December 30, 2020, 1:57pm UTC](https://forum.cmascenter.org/t/how-to-run-cmaq-isam/1606/10 "2020-12-30T13:57:07Z")
@Catalyst2682
I setup my isam control file as Sergey mentioned above, and I’ve successfully run CMAQ v5.3.2-ISAM.
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### Author:  [@Catalyst2682](https://forum.cmascenter.org/u/Catalyst2682)
#### Post date: [December 30, 2020, 2:13pm UTC](https://forum.cmascenter.org/t/how-to-run-cmaq-isam/1606/11 "2020-12-30T14:13:10Z")
@ykaore
I have ran it successfully too.
Thanks and kind regards,
Catalyst