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New version of Release Scripts #40

Merged
merged 53 commits into from
Jun 23, 2017
Merged

New version of Release Scripts #40

merged 53 commits into from
Jun 23, 2017

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bnmurphy
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Now both repository-based and external project-based workflows are accommodated. Also, all mentions of EPA or site-specific options are removed.

bnmurphy and others added 30 commits May 9, 2017 17:16
 On branch BC_opt
	modified:   PARIO/boundary.f
	modified:   PARIO/interpol.f
	modified:   PARIO/parutilio.f
	modified:   PARIO/pinterpb.f
	modified:   hadv/yamo/rdbcon.F
 On branch BC_opt
    The BC IO-API file header was being read every time a species
    array was requested. This ended up consuming 50-60% of the runtime
    on a 100x80 domain.

    modified:   src/PARIO/pinterpb.f
	modified:   src/hadv/yamo/advbc_map.F
	modified:   src/hadv/yamo/hadvyppm.F
	modified:   src/hadv/yamo/rdbcon.F
	modified:   src/hadv/yamo/x_yamo.F
	modified:   src/hadv/yamo/y_yamo.F
 On branch BC_opt
	modified:   src/hadv/yamo/rdbcon.F
Contributed by: J. Gipson
Revision History: C. Nolte April 2016
                  C. Nolte and C. Hogrefe, June 2017:
		      replace ioapi EXT files with M3UTILIO
		      bug fix in variable name checking
Block_extract extracts time series of 1 or more variables from 1 or more
(up to 99) IOAPI files for a specified range of cells.
There can be multiple files covering an extended time period, but all files
must have the same header (grid, layers, variable names, etc.).
Program produces two text files.
One file (specfile) lists the variables that were extracted.
The second text file (OUTFILE) contains the time series of the extracted variables with columns.
	new file:   ck_ctms.f
	new file:   cksetup.f
	new file:   driver.f
	new file:   get_gridval.f
	new file:   get_timout.f
	new file:   module_envvar.f
	new file:   module_file.f
	new file:   module_grid.f
	new file:   module_tstep.f
	new file:   output.f
	new file:   process.f
	deleted:    POST/appendwrf/scripts/run.appendwrf
	new file:   POST/appendwrf/scripts/run.appendwrf.csh
	modified:   POST/bldoverlay/README.md
	new file:   POST/bldoverlay/inputs/tz.csv
	deleted:    POST/bldoverlay/scripts/run.bldoverlay
	new file:   POST/bldoverlay/scripts/run.bldoverlay.csh
	new file:   README.md
	new file:   scripts/run.block_extract
 On branch BC_opt
	modified:   CCTM/src/hadv/yamo/rdbcon.F
 On branch BC_opt
	modified:   src/hadv/yamo/hadvyppm.F
	modified:   POST/appendwrf/scripts/run.appendwrf.csh
	new file:   POST/bldoverlay/inputs/ozone_overlay_input_sample.csv
	modified:   POST/bldoverlay/scripts/run.bldoverlay.csh
	deleted:    POST/block_extract/scripts/run.block_extract
	new file:   POST/block_extract/scripts/run.block_extract.csh
	deleted:    POST/hr2day/scripts/run.hr2day.make8hrmax
	new file:   POST/hr2day/scripts/run.hr2day.make8hrmax.csh
	deleted:    POST/sitecmp_dailyo3/scripts/run.sitecmp.AQS_Daily
	deleted:    POST/sitecmp_dailyo3/scripts/run.sitecmp.CASTNET_Daily
	new file:   POST/sitecmp_dailyo3/scripts/run.sitecmp_dailyo3_AQS.csh
	new file:   POST/sitecmp_dailyo3/scripts/run.sitecmp_dailyo3_CASTNET.csh
	renamed:    POST/writesite/scripts/sites.txt -> POST/writesite/inputs/sites.txt
	deleted:    POST/writesite/scripts/run.writesite
	new file:   POST/writesite/scripts/run.writesite.csh
	deleted:    POST/writesite/scripts/tz.csv
	deleted:    ../../combine/scripts/run.combine.Uncoupled
	new file:   ../../combine/scripts/run.combine.uncoupled.csh
	renamed:    ../../sitecmp/scripts/CSN/run.sitecmp.CSN.2009.and.earlier -> ../../sitecmp/scripts/CSN/run.sitecmp.CSN.2009.and.earlier.csh
	renamed:    ../../sitecmp/scripts/CSN/run.sitecmp.CSN.2010 -> ../../sitecmp/scripts/CSN/run.sitecmp.CSN.2010.csh
	renamed:    ../../sitecmp/scripts/CSN/run.sitecmp.CSN.2011.and.later -> ../../sitecmp/scripts/CSN/run.sitecmp.CSN.2011.and.later.csh
	deleted:    ../../sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Daily.2007.and.earlier
	new file:   ../../sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Daily.2007.and.earlier.csh
	deleted:    ../../sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Daily.2008.and.later
	new file:   ../../sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Daily.2008.and.later.csh
	renamed:    ../../sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Hourly.2004.and.earlier -> ../../sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Hourly.2004.and.earlier.csh
	renamed:    ../../sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Hourly.2005 -> ../../sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Hourly.2005.csh
	renamed:    ../../sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Hourly.2006.to.2012 -> ../../sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Hourly.2006.to.2012.csh
	renamed:    ../../sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Hourly.2013.and.later -> ../../sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Hourly.2013.and.later.csh
	deleted:    ../../sitecmp/scripts/run.sitecmp.AERONET
	new file:   ../../sitecmp/scripts/run.sitecmp.AERONET.csh
	deleted:    ../../sitecmp/scripts/run.sitecmp.AMON
	new file:   ../../sitecmp/scripts/run.sitecmp.AMON.csh
	renamed:    ../../sitecmp/scripts/run.sitecmp.AQS_Hourly -> ../../sitecmp/scripts/run.sitecmp.AQS.Hourly.csh
	deleted:    ../../sitecmp/scripts/run.sitecmp.CASTNET_Hourly
	new file:   ../../sitecmp/scripts/run.sitecmp.CASTNET_Hourly.csh
	renamed:    ../../sitecmp/scripts/run.sitecmp.CASTNET_Weekly -> ../../sitecmp/scripts/run.sitecmp.CASTNET_Weekly.csh
	renamed:    ../../sitecmp/scripts/run.sitecmp.IMPROVE -> ../../sitecmp/scripts/run.sitecmp.IMPROVE.csh
	renamed:    ../../sitecmp/scripts/run.sitecmp.NADP -> ../../sitecmp/scripts/run.sitecmp.NADP.csh
…plate.

	renamed:    ../../appendwrf/scripts/run.appendwrf.csh -> ../../appendwrf/scripts/run_appendwrf.csh
	renamed:    ../../bldoverlay/scripts/run.bldoverlay.csh -> ../../bldoverlay/scripts/run_bldoverlay.csh
	renamed:    ../../block_extract/scripts/run.block_extract.csh -> ../../block_extract/scripts/run_block_extract.csh
	renamed:    ../../combine/scripts/run.combine.uncoupled.csh -> ../../combine/scripts/run_combine_uncoupled.csh
	renamed:    ../../hr2day/scripts/run.hr2day.make8hrmax.csh -> ../../hr2day/scripts/run_hr2day.csh
	renamed:    run.sitecmp.AQS.Hourly.csh -> run_sitecmp_AQS_Hourly.csh
	renamed:    ../../sitecmp_dailyo3/scripts/run.sitecmp_dailyo3_AQS.csh -> ../../sitecmp_dailyo3/scripts/run_sitecmp_dailyo3_AQS.csh
	renamed:    ../../sitecmp_dailyo3/scripts/run.sitecmp_dailyo3_CASTNET.csh -> ../../sitecmp_dailyo3/scripts/run_sitecmp_dailyo3_CASTNET.csh
	renamed:    ../../writesite/scripts/run.writesite.csh -> ../../writesite/scripts/run_writesite.csh
updated the bldit scripts for appendwrf, bldoverlay,
hr2day, sitecmp, sitecmp_dailyo3, and writesite for
the CMAQ_v52 release architecture using a template
developed by bmurphy for combine
/home/bmurphy/cmaq_repos/New_Scripts/June2017_release/CMAQ_REPO/POST/combine/scripts/bldit_combine.csh

While testing the revised bldit script, discovered a bug in
hr2day/src/hr2day.F

The code was using a local variable "lasttime" that is already defined
in the M3UTILIO module and the intel compiler exited with an error message.

Updated the code to replace "firstdate", "firsttime", "lastdate", and
"lasttime" with "first_date", "first_time", "last_date", and "last_time"

        added:      appendwrf/scripts/bldit_appendwrf.csh
        added:      bldoverlay/scripts/bldit_bldoverlay.csh
        added:      block_extract/scripts/bldit_block_extract.csh
        added:      combine/scripts/bldit_combine.csh
        added:      hr2day/scripts/bldit_hr2day.csh
        added:      sitecmp/scripts/bldit_sitecmp.csh
        added:      sitecmp_dailyo3/scripts/bldit_sitecmp_dailyo3.csh
        added:      writesite/scripts/bldit_writesite.csh
	deleted:    appendwrf/scripts/bldit.appendwrf
	deleted:    bldoverlay/scripts/bldit.bldoverlay
	deleted:    combine/scripts/bldit.combine
	deleted:    hr2day/scripts/bldit.hr2day
	deleted:    sitecmp/scripts/bldit.sitecmp
	deleted:    sitecmp_dailyo3/scripts/bldit.sitecmp_dailyo3
	deleted:    writesite/scripts/bldit.writesite
	modified:   hr2day/src/hr2day.F
added new bldit scripts based on the bldit_combine.csh
template developed by bmurphy in
/home/bmurphy/cmaq_repos/New_Scripts/June2017_Release/CMAQ_REPO/POST/combine/scripts/bldit_combine.csh

The new bldit scripts executed successfully and built the executables for
appendwrf, bldoverlay, block_extract, combine, hr2day, sitecmp,
sitecmp_dailyo3, and writesite for intel, pgi, and gcc

	new file:   POST/appendwrf/scripts/bldit_appendwrf.csh
	new file:   POST/bldoverlay/scripts/bldit_bldoverlay.csh
	new file:   POST/block_extract/scripts/bldit_block_extract.csh
	new file:   POST/combine/scripts/bldit_combine.csh
	new file:   POST/hr2day/scripts/bldit_hr2day.csh
	new file:   POST/sitecmp/scripts/bldit_sitecmp.csh
	new file:   POST/sitecmp_dailyo3/scripts/bldit_sitecmp_dailyo3.csh
	new file:   POST/writesite/scripts/bldit_writesite.csh
…s are needed for differetn network (e.g. AQS, CSN, IMPROVE, NADP). The changes needed for the run script are captured in the new README.md file.

	deleted:    CSN/README
	deleted:    CSN/run.sitecmp.CSN.2009.and.earlier.csh
	deleted:    CSN/run.sitecmp.CSN.2010.csh
	deleted:    CSN/run.sitecmp.CSN.2011.and.later.csh
	new file:   README.md
	deleted:    SEARCH/README
	deleted:    SEARCH/run.sitecmp.SEARCH_Daily.2007.and.earlier.csh
	deleted:    SEARCH/run.sitecmp.SEARCH_Daily.2008.and.later.csh
	deleted:    SEARCH/run.sitecmp.SEARCH_Hourly.2004.and.earlier.csh
	deleted:    SEARCH/run.sitecmp.SEARCH_Hourly.2005.csh
	deleted:    SEARCH/run.sitecmp.SEARCH_Hourly.2006.to.2012.csh
	deleted:    SEARCH/run.sitecmp.SEARCH_Hourly.2013.and.later.csh
	deleted:    run.sitecmp.AERONET.csh
	deleted:    run.sitecmp.AMON.csh
	deleted:    run.sitecmp.CASTNET_Hourly.csh
	deleted:    run.sitecmp.CASTNET_Weekly.csh
	deleted:    run.sitecmp.IMPROVE.csh
	deleted:    run.sitecmp.NADP.csh
	modified:   run_sitecmp_AQS_Hourly.csh
Merged with release_repo master branch.

	new file:   CCTM/scripts/bldit_cctm.csh
	new file:   CCTM/scripts/run_cctm.csh
	deleted:    CCTM/scripts_sol/bldit.cctm
	deleted:    CCTM/scripts_sol/outck.q
	deleted:    CCTM/scripts_sol/run.intel
	modified:   CCTM/src/emis/emis/DUST_EMIS.F
	modified:   CCTM/src/util/util/setup_logdev.F
	modified:   POST/combine/scripts/bldit_combine.csh
	new file:   POST/combine/scripts/run_combine.csh
	deleted:    UTIL/bldmake/src/Makefile
	modified:   UTIL/bldmake/src/bldmake.f
	modified:   UTIL/bldmake/src/cfg_module.f
	deleted:    config.cmaq
	new file:   config_cmaq.csh
	new file:   extract_scripts.csh
	modified:   README.md
	modified:   run_sitecmp_AQS_Hourly.csh

In run_sitecmp_AQS_Hourly.csh added a line to extract NO observations.
In README.md corrected model/observation matching for the CSN network based on the latest AMET_species_list.R file from W. Appel.  Corrected the column names in the CSN Views data files for OC and Total PM2.5 for different years.
bnmurphy and others added 23 commits June 19, 2017 09:54
 On branch BC_opt
	modified:   config_cmaq.csh
Inserted line to initialize TROPO_O3_COLUMN to zero.
 	modified:   CCTM/src/phot/inline/CLOUD_OPTICS.F
 	modified:   CCTM/src/phot/inline/PHOTOLYSIS_ALBEDO.F
 	modified:   CCTM/src/phot/inline/PHOT_MET_DATA.F
 	modified:   CCTM/src/phot/inline/o3totcol.f
 	modified:   CCTM/src/phot/inline/phot.F
        -removed several implicit conversions between types
        -tests with intel version 11 compiler showed no differences
        in predictions when using the default FAST_OPTICS options
 	modified:   CCTM/src/twoway/twoway_rrtmg_aero_optics.F90
        -removed several implicit conversions between types
        -tests showed up to 10% difference in aerosol optical depths
        when using the MIE_OPTICS option
 On branch BC_opt
	modified:   config_cmaq.csh
 	modified:   CCTM/src/phot/inline/CLOUD_OPTICS.F
 	modified:   CCTM/src/phot/inline/PHOT_MOD.F
 	modified:   CCTM/src/phot/inline/PHOTOLYSIS_ALBEDO.F
 	modified:   CCTM/src/phot/inline/PHOT_MET_DATA.F
 	modified:   CCTM/src/phot/inline/o3totcol.f
 	modified:   CCTM/src/phot/inline/phot.F
        -removed several implicit conversions between types
        -tests with intel version 11 compiler showed no differences
        in predictions when using the default FAST_OPTICS options
 	modified:   CCTM/src/twoway/twoway_rrtmg_aero_optics.F90
        -removed several implicit conversions between types
        -tests showed up to 10% difference in aerosol optical depths
        when using the MIE_OPTICS option
…g_cmaq.csh rather than config.cmaq to be consistent with the repo.

	modified:   appendwrf/scripts/run_appendwrf.csh
	modified:   bldoverlay/scripts/run_bldoverlay.csh
	modified:   block_extract/scripts/run_block_extract.csh
	renamed:    combine/scripts/run_combine_uncoupled.csh -> combine/scripts/run_combine.csh
	modified:   hr2day/scripts/run_hr2day.csh
	modified:   sitecmp/scripts/run_sitecmp_AQS_Hourly.csh
	modified:   sitecmp_dailyo3/scripts/run_sitecmp_dailyo3_AQS.csh
	modified:   sitecmp_dailyo3/scripts/run_sitecmp_dailyo3_CASTNET.csh
	modified:   writesite/scripts/run_writesite.csh
 On branch release_scripts
	modified:   CCTM/scripts/bldit_cctm.csh
	renamed:    extract_scripts.csh -> bldit_project.csh
	modified:   config_cmaq.csh

	modified:   .gitignore

	modified:   CCTM/scripts/run_cctm.csh
	modified:   POST/combine/scripts/bldit_combine.csh
 On branch release_scripts
	deleted:    POST/combine/scripts/.run_combine.csh.swp
	modified:   bldit_project.csh
 On branch release_scripts
	modified:   .gitignore
	deleted:    CCTM/scripts/.run_cctm.csh.swp
	modified:   CCTM/scripts/bldit_cctm.csh
	modified:   CCTM/scripts/run_cctm.csh
	renamed:    PREP/agdust/scripts/run.calmap -> PREP/agdust/scripts/run_calmap.csh
	renamed:    PREP/bc/BCON/scripts_sol/bldit.bcon.1 -> PREP/bc/BCON/scripts/bldit.bcon.1
	renamed:    PREP/bc/BCON/scripts_sol/bldit.bcon -> PREP/bc/BCON/scripts/bldit_bcon.csh
	renamed:    PREP/ic/ICON/scripts/bldit.icon -> PREP/ic/ICON/scripts/bldit_icon.csh
	renamed:    PREP/mcip/scripts/run.mcip -> PREP/mcip/scripts/run_mcip.csh
	modified:   bldit_project.csh
	modified:   config_cmaq.csh
 On branch release_scripts
	modified:   POST/appendwrf/scripts/bldit_appendwrf.csh
	modified:   POST/appendwrf/scripts/run_appendwrf.csh
	modified:   POST/bldoverlay/scripts/bldit_bldoverlay.csh
	modified:   POST/bldoverlay/scripts/run_bldoverlay.csh
	modified:   POST/block_extract/scripts/bldit_block_extract.csh
	modified:   POST/block_extract/scripts/run_block_extract.csh
	new file:   POST/combine/scripts/.run_combine.csh.swp
	modified:   POST/combine/scripts/bldit_combine.csh
	modified:   POST/combine/scripts/run_combine.csh
	modified:   POST/hr2day/scripts/bldit_hr2day.csh
	modified:   POST/hr2day/scripts/run_hr2day.csh
	modified:   POST/sitecmp/scripts/bldit_sitecmp.csh
	modified:   POST/sitecmp/scripts/run_sitecmp_AQS_Hourly.csh
	modified:   POST/sitecmp_dailyo3/scripts/bldit_sitecmp_dailyo3.csh
	modified:   POST/sitecmp_dailyo3/scripts/run_sitecmp_dailyo3_AQS.csh
	modified:   POST/sitecmp_dailyo3/scripts/run_sitecmp_dailyo3_CASTNET.csh
	modified:   POST/writesite/scripts/bldit_writesite.csh
	modified:   POST/writesite/scripts/run_writesite.csh
	modified:   bldit_project.csh
 On branch release_scripts
	modified:   POST/appendwrf/scripts/run_appendwrf.csh
	modified:   POST/bldoverlay/scripts/run_bldoverlay.csh
	modified:   POST/block_extract/scripts/run_block_extract.csh
	modified:   POST/combine/scripts/.run_combine.csh.swp
	modified:   POST/combine/scripts/run_combine.csh
	modified:   POST/hr2day/scripts/run_hr2day.csh
	modified:   POST/sitecmp/scripts/run_sitecmp_AQS_Hourly.csh
	modified:   POST/sitecmp_dailyo3/scripts/run_sitecmp_dailyo3_AQS.csh
	modified:   POST/sitecmp_dailyo3/scripts/run_sitecmp_dailyo3_CASTNET.csh
	modified:   POST/writesite/scripts/run_writesite.csh
 On branch release_scripts
	modified:   .gitignore
	modified:   CCTM/scripts/run_cctm.csh
	deleted:    POST/combine/scripts/.run_combine.csh.swp
	modified:   bldit_project.csh
 On branch release_scripts
	modified:   CCTM/scripts/bldit_cctm.csh
	modified:   UTIL/bldmake/src/bldmake.f
	modified:   UTIL/bldmake/src/cfg_module.f
	modified:   bldit_project.csh
	modified:   config_cmaq.csh
 On branch release_scripts
	modified:   POST/appendwrf/scripts/bldit_appendwrf.csh
	modified:   POST/bldoverlay/scripts/bldit_bldoverlay.csh
	modified:   POST/block_extract/scripts/bldit_block_extract.csh
	modified:   POST/combine/scripts/bldit_combine.csh
	modified:   POST/hr2day/scripts/bldit_hr2day.csh
	modified:   POST/sitecmp/scripts/bldit_sitecmp.csh
	modified:   POST/sitecmp_dailyo3/scripts/bldit_sitecmp_dailyo3.csh
	modified:   POST/writesite/scripts/bldit_writesite.csh
	modified:   bldit_project.csh
…elopment

Conflicts:
	POST/appendwrf/scripts/bldit.appendwrf
	POST/appendwrf/scripts/run.appendwrf
	POST/bldoverlay/inputs/tz.csv
	POST/bldoverlay/scripts/bldit.bldoverlay
	POST/bldoverlay/scripts/run.bldoverlay
	POST/hr2day/inputs/tz.csv
	POST/hr2day/scripts/bldit.hr2day
	POST/hr2day/scripts/run.hr2day.make8hrmax
	POST/sitecmp/scripts/CSN/run.sitecmp.CSN.2009.and.earlier
	POST/sitecmp/scripts/CSN/run.sitecmp.CSN.2010
	POST/sitecmp/scripts/CSN/run.sitecmp.CSN.2011.and.later
	POST/sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Daily.2007.and.earlier
	POST/sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Daily.2008.and.later
	POST/sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Hourly.2004.and.earlier
	POST/sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Hourly.2005
	POST/sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Hourly.2006.to.2012
	POST/sitecmp/scripts/SEARCH/run.sitecmp.SEARCH_Hourly.2013.and.later
	POST/sitecmp/scripts/bldit.sitecmp
	POST/sitecmp/scripts/run.sitecmp.AERONET
	POST/sitecmp/scripts/run.sitecmp.AMON
	POST/sitecmp/scripts/run.sitecmp.AQS_Hourly
	POST/sitecmp/scripts/run.sitecmp.CASTNET_Hourly
	POST/sitecmp/scripts/run.sitecmp.CASTNET_Weekly
	POST/sitecmp/scripts/run.sitecmp.IMPROVE
	POST/sitecmp/scripts/run.sitecmp.NADP
	POST/sitecmp_dailyo3/scripts/bldit.sitecmp_dailyo3
	POST/sitecmp_dailyo3/scripts/run.sitecmp.AQS_Daily
	POST/sitecmp_dailyo3/scripts/run.sitecmp.CASTNET_Daily
	POST/writesite/inputs/sites.txt
	POST/writesite/scripts/bldit.writesite
	POST/writesite/scripts/run.writesite
	POST/writesite/scripts/tz.csv
	PREP/bc/BCON/scripts/bldit.bcon.1
	PREP/bc/BCON/scripts/bldit_bcon.csh
	PREP/bc/BCON/scripts_sol/bldit.bcon
	PREP/bcon/scripts/bldit.bcon
	PREP/ic/ICON/scripts/bldit_icon.csh
	extract_scripts.csh
@bnmurphy bnmurphy self-assigned this Jun 23, 2017
@bnmurphy bnmurphy merged commit a6aff60 into USEPA:5.2 Jun 23, 2017
lizadams pushed a commit to lizadams/CMAQ that referenced this pull request Nov 25, 2019
CMAQv53 documentation updates from public repo
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4 participants