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More cleanup of app scripts, add simtime to logging #508

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merged 3 commits into from
Sep 21, 2023
Merged

More cleanup of app scripts, add simtime to logging #508

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3809ba8
More cleanup of app scripts
mathomp4 Aug 29, 2023
1554ec3
Add comment, clean spaces
mathomp4 Aug 29, 2023
10c2f20
Merge branch 'develop' into feature/mathomp4/more-cleanup
sdrabenh Sep 21, 2023
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6 changes: 0 additions & 6 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -44,12 +44,6 @@ install (
DESTINATION etc
)

if(HYDROSTATIC)
set(CFG_HYDROSTATIC TRUE)
else()
set(CFG_HYDROSTATIC FALSE)
endif()

if(INSTALL_SOURCE_TARFILE)
set(CFG_INSTALL_SOURCE_TARFILE TRUE)
else()
Expand Down
17 changes: 7 additions & 10 deletions gcm_run.j
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Original file line number Diff line number Diff line change
Expand Up @@ -841,16 +841,16 @@ if ( $DNA_TRUE == 0 && -e DNA_ExtData.rc ) /bin/mv
set ACHEM_TRUE = `grep -i '^\s*ENABLE_ACHEM:\s*\.TRUE\.' GEOS_ChemGridComp.rc | wc -l`
if ( $ACHEM_TRUE == 0 && -e GEOSachem_ExtData.rc ) /bin/mv GEOSachem_ExtData.rc GEOSachem_ExtData.rc.NOT_USED

@MP_NO_USE_WSUB# 1MOM and GFDL microphysics do not use WSUB_CLIM
@MP_NO_USE_WSUB# -------------------------------------------------
@MP_TURN_OFF_WSUB_EXTDATA# 1MOM and GFDL microphysics do not use WSUB_CLIM
@MP_TURN_OFF_WSUB_EXTDATA# -------------------------------------------------
if ($EXTDATA2G_TRUE == 0 ) then
@MP_NO_USE_WSUB/bin/mv WSUB_ExtData.rc WSUB_ExtData.tmp
@MP_NO_USE_WSUBcat WSUB_ExtData.tmp | sed -e '/^WSUB_CLIM/ s#ExtData.*#/dev/null#' > WSUB_ExtData.rc
@MP_TURN_OFF_WSUB_EXTDATA/bin/mv WSUB_ExtData.rc WSUB_ExtData.tmp
@MP_TURN_OFF_WSUB_EXTDATAcat WSUB_ExtData.tmp | sed -e '/^WSUB_CLIM/ s#ExtData.*#/dev/null#' > WSUB_ExtData.rc
else
@MP_NO_USE_WSUB/bin/mv WSUB_ExtData.yaml WSUB_ExtData.tmp
@MP_NO_USE_WSUBcat WSUB_ExtData.tmp | sed -e '/collection:/ s#WSUB_SWclim.*#/dev/null#' > WSUB_ExtData.yaml
@MP_TURN_OFF_WSUB_EXTDATA/bin/mv WSUB_ExtData.yaml WSUB_ExtData.tmp
@MP_TURN_OFF_WSUB_EXTDATAcat WSUB_ExtData.tmp | sed -e '/collection:/ s#WSUB_SWclim.*#/dev/null#' > WSUB_ExtData.yaml
endif
@MP_NO_USE_WSUB/bin/rm WSUB_ExtData.tmp
@MP_TURN_OFF_WSUB_EXTDATA/bin/rm WSUB_ExtData.tmp

# Generate the complete ExtData.rc
# --------------------------------
Expand Down Expand Up @@ -892,9 +892,6 @@ setenv YEAR $yearc

if (! -e tile.bin) then
$GEOSBIN/binarytile.x tile.data tile.bin
### @MIT $GEOSBIN/binarytile.x tile_hist.data tile_hist.bin
### @MOM5 $GEOSBIN/binarytile.x tile_hist.data tile_hist.bin
### @MOM6 $GEOSBIN/binarytile.x tile_hist.data tile_hist.bin
endif

# If running in dual ocean mode, link sst and fraci data here
Expand Down
35 changes: 5 additions & 30 deletions gcm_setup
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Original file line number Diff line number Diff line change
Expand Up @@ -1391,26 +1391,17 @@ set GFDL_USE_CCN = "use_ccn = .true."

# BACM_1M and GFDL do not use WSUB_CLIM, so this eliminates a regrid
if ( "$CLDMICRO" == "BACM_1M" | "$CLDMICRO" == "GFDL_1M" ) then
set MP_NO_USE_WSUB = ""
set MP_TURN_OFF_WSUB_EXTDATA = ""
else
set MP_NO_USE_WSUB = "#DELETE#"
set MP_TURN_OFF_WSUB_EXTDATA = "#DELETE#"
endif

# Settings for fvcore_layout.rc
if ( "$USE_HYDROSTATIC" == "TRUE" ) then
set FV_MAKENH = "Make_NH = .F."
set FV_HYDRO = "hydrostatic = .T."
else
# Logic for NH runs based on build type
if ( "$DEFAULT_HYDROSTATIC" == "TRUE") then
# If you built for hydrostatic, but want an NH run, run make_nh
set FV_MAKENH = "Make_NH = .T."
else
# If you built for non-hydrostatic and want an NH run, do not run
# NOTE: If you run regrid.pl it will make restarts that should trigger
# make_nh automatically in FV3
set FV_MAKENH = "Make_NH = .F."
endif
set FV_MAKENH = "Make_NH = .T."
set FV_HYDRO = "hydrostatic = .F."
if ( "$CLDMICRO" == "GFDL_1M" ) then
set GFDL_HYDRO = ".FALSE."
Expand Down Expand Up @@ -1631,23 +1622,7 @@ while( $check == FALSE )
# Check to see if the HISTORY template exists in the $ETCDIR
if( -f $ETCDIR/$HISTORY_TEMPLATE ) then
set check = TRUE
set TMPHIST1 = `mktemp`
/bin/cp -f $ETCDIR/$HISTORY_TEMPLATE $TMPHIST1

set EXPID_old = `grep "EXPID:" $TMPHIST1 | cut -d: -f2`
set EXPDSC_old = `grep "EXPDSC:" $TMPHIST1 | cut -d: -f2`

set TMPCMD = `mktemp`
set string = "EXPID:"
echo cat $TMPHIST1 \| awk \'\{if \( \$1 \~ \"${string}\" \) \
\{sub \( \"${EXPID_old}\" , \"${EXPID}\" \)\;print\} else print\}\' \> $TMPHIST > $TMPCMD
chmod +x $TMPCMD
$TMPCMD
/bin/rm -f $TMPCMD
/bin/mv -f $TMPHIST $TMPHIST1
cat $TMPHIST1 | sed -e "s|${EXPDSC_old}|${EXPDSC}|g" > $TMPHIST
/bin/rm -f $TMPHIST1

/bin/cp -f $ETCDIR/$HISTORY_TEMPLATE $TMPHIST
# else check if the file exists (assuming they sent in full path)
else if( -e $HISTORY_TEMPLATE ) then
set check = TRUE
Expand Down Expand Up @@ -2430,7 +2405,7 @@ s/@ANALYZE_TS/0/g

s/@LSM_CHOICE/$LSM_CHOICE/g

s/@MP_NO_USE_WSUB/$MP_NO_USE_WSUB/g
s/@MP_TURN_OFF_WSUB_EXTDATA/$MP_TURN_OFF_WSUB_EXTDATA/g

s?@BACM_1M_?$BACM_1M_?g
s?@GFDL_1M_?$GFDL_1M_?g
Expand Down
35 changes: 5 additions & 30 deletions geoschemchem_setup
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Original file line number Diff line number Diff line change
Expand Up @@ -1406,26 +1406,17 @@ set GFDL_USE_CCN = "use_ccn = .true."

# BACM_1M and GFDL do not use WSUB_CLIM, so this eliminates a regrid
if ( "$CLDMICRO" == "BACM_1M" | "$CLDMICRO" == "GFDL_1M" ) then
set MP_NO_USE_WSUB = ""
set MP_TURN_OFF_WSUB_EXTDATA = ""
else
set MP_NO_USE_WSUB = "#DELETE#"
set MP_TURN_OFF_WSUB_EXTDATA = "#DELETE#"
endif

# Settings for fvcore_layout.rc
if ( "$USE_HYDROSTATIC" == "TRUE" ) then
set FV_MAKENH = "Make_NH = .F."
set FV_HYDRO = "hydrostatic = .T."
else
# Logic for NH runs based on build type
if ( "$DEFAULT_HYDROSTATIC" == "TRUE") then
# If you built for hydrostatic, but want an NH run, run make_nh
set FV_MAKENH = "Make_NH = .T."
else
# If you built for non-hydrostatic and want an NH run, do not run
# NOTE: If you run regrid.pl it will make restarts that should trigger
# make_nh automatically in FV3
set FV_MAKENH = "Make_NH = .F."
endif
set FV_MAKENH = "Make_NH = .T."
set FV_HYDRO = "hydrostatic = .F."
if ( "$CLDMICRO" == "GFDL_1M" ) then
set GFDL_HYDRO = ".FALSE."
Expand Down Expand Up @@ -1661,23 +1652,7 @@ while( $check == FALSE )
# Check to see if the HISTORY template exists in the $ETCDIR
if( -f $ETCDIR/$HISTORY_TEMPLATE ) then
set check = TRUE
set TMPHIST1 = `mktemp`
/bin/cp -f $ETCDIR/$HISTORY_TEMPLATE $TMPHIST1

set EXPID_old = `grep "EXPID:" $TMPHIST1 | cut -d: -f2`
set EXPDSC_old = `grep "EXPDSC:" $TMPHIST1 | cut -d: -f2`

set TMPCMD = `mktemp`
set string = "EXPID:"
echo cat $TMPHIST1 \| awk \'\{if \( \$1 \~ \"${string}\" \) \
\{sub \( \"${EXPID_old}\" , \"${EXPID}\" \)\;print\} else print\}\' \> $TMPHIST > $TMPCMD
chmod +x $TMPCMD
$TMPCMD
/bin/rm -f $TMPCMD
/bin/mv -f $TMPHIST $TMPHIST1
cat $TMPHIST1 | sed -e "s|${EXPDSC_old}|${EXPDSC}|g" > $TMPHIST
/bin/rm -f $TMPHIST1

/bin/cp -f $ETCDIR/$HISTORY_TEMPLATE $TMPHIST
# else check if the file exists (assuming they sent in full path)
else if( -e $HISTORY_TEMPLATE ) then
set check = TRUE
Expand Down Expand Up @@ -2462,7 +2437,7 @@ s/@ANALYZE_TS/0/g

s/@LSM_CHOICE/$LSM_CHOICE/g

s/@MP_NO_USE_WSUB/$MP_NO_USE_WSUB/g
s/@MP_TURN_OFF_WSUB_EXTDATA/$MP_TURN_OFF_WSUB_EXTDATA/g

s?@BACM_1M_?$BACM_1M_?g
s?@GFDL_1M_?$GFDL_1M_?g
Expand Down
35 changes: 5 additions & 30 deletions gmichem_setup
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Original file line number Diff line number Diff line change
Expand Up @@ -1503,26 +1503,17 @@ set GFDL_USE_CCN = "use_ccn = .true."

# BACM_1M and GFDL do not use WSUB_CLIM, so this eliminates a regrid
if ( "$CLDMICRO" == "BACM_1M" | "$CLDMICRO" == "GFDL_1M" ) then
set MP_NO_USE_WSUB = ""
set MP_TURN_OFF_WSUB_EXTDATA = ""
else
set MP_NO_USE_WSUB = "#DELETE#"
set MP_TURN_OFF_WSUB_EXTDATA = "#DELETE#"
endif

# Settings for fvcore_layout.rc
if ( "$USE_HYDROSTATIC" == "TRUE" ) then
set FV_MAKENH = "Make_NH = .F."
set FV_HYDRO = "hydrostatic = .T."
else
# Logic for NH runs based on build type
if ( "$DEFAULT_HYDROSTATIC" == "TRUE") then
# If you built for hydrostatic, but want an NH run, run make_nh
set FV_MAKENH = "Make_NH = .T."
else
# If you built for non-hydrostatic and want an NH run, do not run
# NOTE: If you run regrid.pl it will make restarts that should trigger
# make_nh automatically in FV3
set FV_MAKENH = "Make_NH = .F."
endif
set FV_MAKENH = "Make_NH = .T."
set FV_HYDRO = "hydrostatic = .F."
if ( "$CLDMICRO" == "GFDL_1M" ) then
set GFDL_HYDRO = ".FALSE."
Expand Down Expand Up @@ -1822,23 +1813,7 @@ while( $check == FALSE )
# Check to see if the HISTORY template exists in the $ETCDIR
if( -f $ETCDIR/$HISTORY_TEMPLATE ) then
set check = TRUE
set TMPHIST1 = `mktemp`
/bin/cp -f $ETCDIR/$HISTORY_TEMPLATE $TMPHIST1

set EXPID_old = `grep "EXPID:" $TMPHIST1 | cut -d: -f2`
set EXPDSC_old = `grep "EXPDSC:" $TMPHIST1 | cut -d: -f2`

set TMPCMD = `mktemp`
set string = "EXPID:"
echo cat $TMPHIST1 \| awk \'\{if \( \$1 \~ \"${string}\" \) \
\{sub \( \"${EXPID_old}\" , \"${EXPID}\" \)\;print\} else print\}\' \> $TMPHIST > $TMPCMD
chmod +x $TMPCMD
$TMPCMD
/bin/rm -f $TMPCMD
/bin/mv -f $TMPHIST $TMPHIST1
cat $TMPHIST1 | sed -e "s|${EXPDSC_old}|${EXPDSC}|g" > $TMPHIST
/bin/rm -f $TMPHIST1

/bin/cp -f $ETCDIR/$HISTORY_TEMPLATE $TMPHIST
# else check if the file exists (assuming they sent in full path)
else if( -e $HISTORY_TEMPLATE ) then
set check = TRUE
Expand Down Expand Up @@ -2628,7 +2603,7 @@ s/@ANALYZE_TS/0/g

s/@LSM_CHOICE/$LSM_CHOICE/g

s/@MP_NO_USE_WSUB/$MP_NO_USE_WSUB/g
s/@MP_TURN_OFF_WSUB_EXTDATA/$MP_TURN_OFF_WSUB_EXTDATA/g

s?@BACM_1M_?$BACM_1M_?g
s?@GFDL_1M_?$GFDL_1M_?g
Expand Down
45 changes: 23 additions & 22 deletions logging.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,25 +4,6 @@ schema_version: 1
#
# https://github.com/GEOS-ESM/MAPL/wiki/How-to-use-the-MAPL-logging-library,-aka-%22pFlogger%22
#
# Let us say you want to get all the debugging loggers
# from ExtData in MAPL. To do this you first want to
# set the 'console' handler below to DEBUG level:
#
# handlers:
# console:
# class: streamhandler
# formatter: basic
# unit: OUTPUT_UNIT
# level: DEBUG
#
# Now we need to add a logger for ExtData. We do this
# by adding the following to the loggers section:
#
# loggers:
# CAP.EXTDATA:
# handlers: [console]
# level: WARNING
# root_level: DEBUG

###############################
locks:
Expand All @@ -34,21 +15,28 @@ locks:
formatters:
plain:
class: Formatter
format: '%(message)a'
format: '%(message)a'

basic:
class: Formatter
format: '%(short_name)a15~: %(level_name)a~: %(message)a'
format: '%(short_name)a15~: %(level_name)a~: %(message)a'

mpi:
class: MpiFormatter
format: '%(mpi_rank)i4.4~: %(name)~: %(level_name)a~: %(message)a'
format: '%(mpi_rank)i4.4~: %(name)~: %(level_name)a~: %(message)a'
comm: MPI_COMM_WORLD

column:
class: Formatter
format: '(%(i)i3.3,%(j)i3.3): %(level_name)'

# This makes an output like:
# AGCM Date: 2000/04/14 Time: 21:00:00 GENERIC: DEBUG: Message
simtime:
class: Formatter
format: '%(simtime)a~ %(short_name)a15~: %(level_name)a~: %(message)a'
datefmt: ' AGCM Date: %(Y)i4.4~/%(M)i2.2~/%(D)i2.2 Time: %(HH)i2.2~:%(MM)i2.2~:%(SS)i2.2'

###############################
handlers:

Expand All @@ -64,6 +52,12 @@ handlers:
unit: OUTPUT_UNIT
level: INFO

console_simtime:
class: streamhandler
formatter: simtime
unit: OUTPUT_UNIT
level: DEBUG

warnings:
class: FileHandler
filename: warnings_and_errors.log
Expand Down Expand Up @@ -122,6 +116,13 @@ loggers:
level: WARNING
root_level: INFO

# To enable this logger, set the console handler
# above to DEBUG level
CAP.EXTDATA:
handlers: [console]
level: WARNING
root_level: DEBUG

# Note: When enabling another logger, make sure
# indentation matches that of the above
# loggers!
Expand Down
35 changes: 5 additions & 30 deletions stratchem_setup
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1406,26 +1406,17 @@ set GFDL_USE_CCN = "use_ccn = .true."

# BACM_1M and GFDL do not use WSUB_CLIM, so this eliminates a regrid
if ( "$CLDMICRO" == "BACM_1M" | "$CLDMICRO" == "GFDL_1M" ) then
set MP_NO_USE_WSUB = ""
set MP_TURN_OFF_WSUB_EXTDATA = ""
else
set MP_NO_USE_WSUB = "#DELETE#"
set MP_TURN_OFF_WSUB_EXTDATA = "#DELETE#"
endif

# Settings for fvcore_layout.rc
if ( "$USE_HYDROSTATIC" == "TRUE" ) then
set FV_MAKENH = "Make_NH = .F."
set FV_HYDRO = "hydrostatic = .T."
else
# Logic for NH runs based on build type
if ( "$DEFAULT_HYDROSTATIC" == "TRUE") then
# If you built for hydrostatic, but want an NH run, run make_nh
set FV_MAKENH = "Make_NH = .T."
else
# If you built for non-hydrostatic and want an NH run, do not run
# NOTE: If you run regrid.pl it will make restarts that should trigger
# make_nh automatically in FV3
set FV_MAKENH = "Make_NH = .F."
endif
set FV_MAKENH = "Make_NH = .T."
set FV_HYDRO = "hydrostatic = .F."
if ( "$CLDMICRO" == "GFDL_1M" ) then
set GFDL_HYDRO = ".FALSE."
Expand Down Expand Up @@ -1646,23 +1637,7 @@ while( $check == FALSE )
# Check to see if the HISTORY template exists in the $ETCDIR
if( -f $ETCDIR/$HISTORY_TEMPLATE ) then
set check = TRUE
set TMPHIST1 = `mktemp`
/bin/cp -f $ETCDIR/$HISTORY_TEMPLATE $TMPHIST1

set EXPID_old = `grep "EXPID:" $TMPHIST1 | cut -d: -f2`
set EXPDSC_old = `grep "EXPDSC:" $TMPHIST1 | cut -d: -f2`

set TMPCMD = `mktemp`
set string = "EXPID:"
echo cat $TMPHIST1 \| awk \'\{if \( \$1 \~ \"${string}\" \) \
\{sub \( \"${EXPID_old}\" , \"${EXPID}\" \)\;print\} else print\}\' \> $TMPHIST > $TMPCMD
chmod +x $TMPCMD
$TMPCMD
/bin/rm -f $TMPCMD
/bin/mv -f $TMPHIST $TMPHIST1
cat $TMPHIST1 | sed -e "s|${EXPDSC_old}|${EXPDSC}|g" > $TMPHIST
/bin/rm -f $TMPHIST1

/bin/cp -f $ETCDIR/$HISTORY_TEMPLATE $TMPHIST
# else check if the file exists (assuming they sent in full path)
else if( -e $HISTORY_TEMPLATE ) then
set check = TRUE
Expand Down Expand Up @@ -2446,7 +2421,7 @@ s/@ANALYZE_TS/0/g

s/@LSM_CHOICE/$LSM_CHOICE/g

s/@MP_NO_USE_WSUB/$MP_NO_USE_WSUB/g
s/@MP_TURN_OFF_WSUB_EXTDATA/$MP_TURN_OFF_WSUB_EXTDATA/g

s?@BACM_1M_?$BACM_1M_?g
s?@GFDL_1M_?$GFDL_1M_?g
Expand Down