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CMAQ v.4.7

CMAQ v.4.7

Last Modified: 09/17 16:07

Description

CMAQ is a community state-of-the-science modeling system for diagnosis and prediction of air pollution.

CMAQ version 4.7 (CMAQv4.7) is released to the user community accompanied by example scripts that invoke a specific configuration of the model. This configuration has been used by U.S. EPA in operational evaluation studies prior to release of the model, and the results of these evaluations accompany this release. There are other features and options within the CMAQ modeling system within this release, beyond this specific model configuration, that have not yet been fully evaluated and documented, that are also available to users.

From: http://www.cmascenter.org/help/model_docs/cmaq/4.7/README.txt

Version

4.7

Plaforms

circe cluster

Download

You'll need to download the appropriate packages from the Community Modeling and Analysis System (CMAS) Center. You'll need to go to the Downloads page and create an account. Follow the directions on the CMAS web site for creating this account. Once it is created, you can log into the downloads section and make the following selections:

Product: CMAQ v.4.7
Type of Computer: Linux-PC
Compiler: Linux Intel Fortran 90

Preliminaries

We'll need to add the appropriate modules to our environment, download, patch and build the appropriate sources. Luckily, this is all done for us with the cmaq-install script. We begin by doing the following

1. Environment Settings

Load the following environment modules

[user@host ~]$ module add apps/cmaq/4.7
[user@host ~]$ module initadd apps/cmaq/4.7

2. Build and Install CMAQ

[user@host ~]$ cmaq-install

Tutorial: Day 1, 32 km Run

At this point, cctm should be ready to run the included 32 km tutorial. You can follow these instructions for running it if you wish to test your installation or get a feel for the program.

Rename and submit the modified script to the queue by issuing

[user@host ~]$ cd $M3HOME/scripts/cctm
[user@host cctm]$ cp run.cctm run.cctm.tut_day1
[user@host cctm]$ qsub run.cctm.tut_day1

Verify that the job completed by checking the contents of output.$JOB_ID. Refer to the GridEngine User's Guide for getting the $JOB_ID number and checking the status of your job.

Note: Data from cctm will be output to /scratch/$USER/cctm rather than $M3DATA/cctm. This is because of a long-standing bug with automounted NFS volumes (like your home directory). The /scratch file system appears to handle the cctm I/O patterns correctly.

Tutorial: Day 2, 32 km Run

(This is directly from the CMAQ Tutorial documentation at http://www.cmascenter.org/help/model_docs/cmaq/4.6/TUTORIAL_PROCEDURE.txt) You will need to make a few changes to the run script for the second day's run. Assuming that you have used the run script as supplied for the first day's run, the following is a "patch" style difference in run.cctm for the second day at 32 km.

Note: The line numbers in this patch format will not match with your run.cctm.sge file! Use the line's context to make the correct changes!

WARNING: Pay very close attention to the contents of this patch! There are subtle changes that you might miss which will cause your run to fail! I would make this easier on you, but when you get to know this program a little more, you'll see its for your own good! You must get used to using patches.

Remember: Left arrow at the beginning of the line means "before the change", right arrow means "after the change"!

Copy run.cctm.tut_day1 to run.cctm.tut_day2 and modify the new file as follows:

7c7
< # Usage: run.cctm >&! cctm_e2a.log &                                  #
---
> # Usage: run.cctm >&! cctm_e2b.log &                                  #
22c22
<  set APPL     = e2a
---
>  set APPL     = e2b
42c42
<  set STDATE   = 1999183       # beginning date
---
>  set STDATE   = 1999184       # beginning date
106,107c106,107
<  set EMISfile  = e_32km_cb4.19990702.ncf
< #set EMISfile  = e_32km_cb4.19990703.ncf
---
> #set EMISfile  = e_32km_cb4.19990702.ncf
>  set EMISfile  = e_32km_cb4.19990703.ncf
114,117c114,117
< #set GC_ICpath = $OUTDIR
< #set GC_ICfile = CCTM_d1bCONC.d1b
<  set GC_ICpath = $M3DATA/icon
<  set GC_ICfile = ICON_cb4_M_32_99TUT02_profile
---
>  set GC_ICpath = $OUTDIR
>  set GC_ICfile = CCTM_e2aCONC.e2a
> #set GC_ICpath = $M3DATA/icon
> #set GC_ICfile = ICON_cb4_M_32_99TUT02_profile

Run the next day's run by submitting the script, run.cctm.tut_day2, to the queue with qsub.

Tutorial: Nested 8k Run

After running both days of the 32 km, you are ready to run the nested 8 km. Again, this section is directly from http://www.cmascenter.org/help/model_docs/cmaq/4.6/TUTORIAL_PROCEDURE.txt

Note: The same rules of thumb from the above patch file still apply!

1. icon

You will need to recompile icon to now use the first 32 km concentration file as input. The following is a "patch" style difference in the bldit.icon script:

42c42
<  set APPL  = e1a
---
>  set APPL  = e3a
59,60c59,60
< #set ModInpt   = ( module m3conc            $Revision; )
<  set ModInpt   = ( module profile           $Revision; )
---
>  set ModInpt   = ( module m3conc            $Revision; )
> #set ModInpt   = ( module profile           $Revision; )
62c62
< #set ModMech   = ( module mc_noop           $Revision; )
---
>  set ModMech   = ( module mc_noop           $Revision; )
64c64
<  set ModMech   = ( module radm2_to_cb4      $Revision; )
---
> #set ModMech   = ( module radm2_to_cb4      $Revision; )

Likewise you will need to modify run.icon, both to point to the new executable and to use the m3conc switch rather than "profile." The following is a patch style difference in run.icon:

7c7
< # Usage: run.icon >&! icon_e2a.log &                                  #
---
> # Usage: run.icon >&! icon_e3a.log &                                  #
23c23
<  set CFG      = e1a
---
>  set CFG      = e3a
35c35
<  setenv GRID_NAME M_32_99TUT02
---
>  setenv GRID_NAME M_08_99TUT02
39c39
<  setenv LAYER_FILE $M3DATA/mcip3/M_32_99NASH/METCRO3D_benchmark2005
---
>  setenv LAYER_FILE $M3DATA/mcip3/M_08_99NASH/METCRO3D_benchmark2005
54,55c54,55
<  set IC = profile      # use default profile file
< #set IC = m3conc       # use CMAQ CTM concentration files (nested runs)
---
> #set IC = profile      # use default profile file
>  set IC = m3conc       # use CMAQ CTM concentration files (nested runs)
115c115
<     setenv CTM_CONC_1 $M3DATA/cctm/CCTM_d1bCONC.d1b
---
>     setenv CTM_CONC_1 $M3DATA/cctm/CCTM_e2aCONC.e2a

2. bcon

You will also need to recompile bcon to now use the 32 km concentration file as input. The following is a "patch" style difference in the bldit.bcon script:

42c42
<  set APPL  = e1a
---
>  set APPL  = e3a
57,58c57,58
< #set ModInpt   = ( module m3conc            $Revision; )
<  set ModInpt   = ( module profile           $Revision; )
---
>  set ModInpt   = ( module m3conc            $Revision; )
> #set ModInpt   = ( module profile           $Revision; )
60c60
< #set ModMech   = ( module mc_noop           $Revision; )
---
>  set ModMech   = ( module mc_noop           $Revision; )
62c62
<  set ModMech   = ( module radm2_to_cb4      $Revision; )
---
> #set ModMech   = ( module radm2_to_cb4      $Revision; )

The following are "patch" style differences in run.bcon, which must now be executed for every day of the nested, 8km runs. The first difference shows how to change the script from running the profile data to the first day of the nested data:

7c7
< # Usage: run.bcon >&! bcon_e2a.log &                                  #
---
> # Usage: run.bcon >&! bcon_e3a.log &                                  #
23c23
<  set CFG      = e1a
---
>  set CFG      = e3a
34c34
<  setenv GRID_NAME M_32_99TUT02
---
>  setenv GRID_NAME M_08_99TUT02
38c38
<  setenv LAYER_FILE $M3DATA/mcip3/M_32_99NASH/METCRO3D_benchmark2005
---
>  setenv LAYER_FILE $M3DATA/mcip3/M_08_99NASH/METCRO3D_benchmark2005
56,57c56,57
<  set BC = profile      # use default profile file
< #set BC = m3conc       # use CMAQ CTM concentration files (nested runs)
---
> #set BC = profile      # use default profile file
>  set BC = m3conc       # use CMAQ CTM concentration files (nested runs)
119c119
<     setenv CTM_CONC_1 $M3DATA/cctm/CCTM_d1bCONC.d1b
---
>     setenv CTM_CONC_1 $M3DATA/cctm/CCTM_e2aCONC.e2a

The second difference shows how to change from the first day of the nest to running the second day:

7c7
< # Usage: run.bcon >&! bcon_e3a.log &                                  #
---
> # Usage: run.bcon >&! bcon_e3b.log &                                  #
64,65c64,65
<     set DATE = 1999183  # July 02, 1999
< #   set DATE = 1999184  # July 03, 1999
---
> #   set DATE = 1999183  # July 02, 1999
>     set DATE = 1999184  # July 03, 1999
119c119
<     setenv CTM_CONC_1 $M3DATA/cctm/CCTM_e2aCONC.e2a
---
>     setenv CTM_CONC_1 $M3DATA/cctm/CCTM_e2aCONC.e2b

3. cctm

Just modify the run script. The first difference shows how to modify the run script run.cctm.tut_day2 from running the second day of the 32 km to the first day of the 8 km nest. Copy run.cctm.tut_day2 to run.cctm.tut_8k_day1 and modify the new file as follows:

7c7
< # Usage: run.cctm >&! cctm_e2b.log &                                  #
---
> # Usage: run.cctm >&! cctm_e3a.log &                                  #
22c22
<  set APPL     = e2b
---
>  set APPL     = e3a
42c42
<  set STDATE   = 1999184       # beginning date
---
>  set STDATE   = 1999183       # beginning date
92c92
<  setenv GRID_NAME M_32_99TUT02
---
>  setenv GRID_NAME M_08_99TUT02
103c103
<  set OCEANfile = SSMASK_tut32
---
>  set OCEANfile = SSMASK_tut08
107,108c107,108
<  set EMISfile  = e_32km_cb4.19990703.ncf
< #set EMISfile  = e_08km_cb4.19990702.ncf
---
> #set EMISfile  = e_32km_cb4.19990703.ncf
>  set EMISfile  = e_08km_cb4.19990702.ncf
114,117c114,117
<  set GC_ICpath = $OUTDIR
<  set GC_ICfile = CCTM_e2aCONC.e2a
< #set GC_ICpath = $M3DATA/icon
< #set GC_ICfile = ICON_cb4_M_32_99TUT02_profile
---
> #set GC_ICpath = $OUTDIR
> #set GC_ICfile = CCTM_e2aCONC.e2a
>  set GC_ICpath = $M3DATA/icon
>  set GC_ICfile = ICON_cb4_M_08_99TUT02_1999183
120c120
<  set GC_BCfile = BCON_cb4_M_32_99TUT02_profile
---
>  set GC_BCfile = BCON_cb4_M_08_99TUT02_1999183
122c122
<  set METpath   = $M3DATA/mcip3/M_32_99NASH
---
>  set METpath   = $M3DATA/mcip3/M_08_99NASH

You should submit this new job to the queue to run. Finally, the differences from the first to the second day of the 8 km runs. Copy run.cctm.tut_8k_day1 to `run.cctm.tut_8k_day2:

7c7
< # Usage: run.cctm >&! cctm_e3a.log &                                  #
---
> # Usage: run.cctm >&! cctm_e3b.log &                                  #
22c22
<  set APPL     = e3a
---
>  set APPL     = e3b
42c42
<  set STDATE   = 1999183       # beginning date
---
>  set STDATE   = 1999184       # beginning date
108,109c108,109
<  set EMISfile  = e_08km_cb4.19990702.ncf
< #set EMISfile  = e_08km_cb4.19990703.ncf
---
> #set EMISfile  = e_08km_cb4.19990702.ncf
>  set EMISfile  = e_08km_cb4.19990703.ncf
114,117c114,117
< #set GC_ICpath = $OUTDIR
< #set GC_ICfile = CCTM_e2aCONC.e2a
<  set GC_ICpath = $M3DATA/icon
<  set GC_ICfile = ICON_cb4_M_08_99TUT02_1999183
---
>  set GC_ICpath = $OUTDIR
>  set GC_ICfile = CCTM_e2aCONC.e3a
> #set GC_ICpath = $M3DATA/icon
> #set GC_ICfile = ICON_cb4_M_08_99TUT02_1999183
120c120
<  set GC_BCfile = BCON_cb4_M_08_99TUT02_1999183
---
>  set GC_BCfile = BCON_cb4_M_08_99TUT02_1999184

You can run the second day of the 8 km run by submitting run.cctm.sge.tut_8k_day2 to the queue.

Other Modules

One other module, procan, is included with the CMAQ distribution. Follow these instructions to build it if needed:

1. procan

Change directory to $M3HOME/scripts/procan

Run the build script by executing

[user@host pdm]$ ./bldit.pacp &> bldit.pacp.out

Check the file bldit.pacp.out to ensure that there are no errors and that the executable compiled correctly. You should see the file PACP_e2a_Linux2_x86_64pg in the current directory.

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