From e0c28ce0e65692ace15521a8db87b99631f562b6 Mon Sep 17 00:00:00 2001
From: Matthew Thompson <matthew.thompson@nasa.gov>
Date: Wed, 21 May 2025 09:45:05 -0400
Subject: [PATCH 1/3] v12: Remove support for mom5

This is one of a set of PRs to remove support for MOM5 in GEOSgcm v12. There are PRs in:

* GEOSgcm:
* GEOS_OceanGridComp:
* GEOSgcm_App:
---
 AGCM.rc.tmpl               | 11 +++--
 gcm_forecast.tmpl          |  2 -
 gcm_regress.j              |  8 ----
 gcm_run.j                  |  9 ----
 gcm_run.j-new_rst_approach |  9 ----
 gcm_run_benchmark.j        |  5 ---
 gcm_setup                  | 68 ++--------------------------
 geoschemchem_setup         | 90 +++++++-------------------------------
 gmichem_setup              | 89 +++++++------------------------------
 linkbcs.tmpl               |  3 --
 stratchem_setup            | 89 +++++++------------------------------
 11 files changed, 58 insertions(+), 325 deletions(-)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index fdd53d9c..db77d505 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -154,7 +154,6 @@ OGCM.JM_WORLD: @OGCM_JM
 OGCM.LM: @OGCM_LM
 @COUPLED OGCM.NX: @OGCM_NX
 @COUPLED OGCM.NY: @OGCM_NY
-@MOM5 OGCM.GRIDSPEC: MAPL_Tripolar.nc
 @MOM6 OGCM.GRIDSPEC: MAPL_Tripolar.nc
 @MIT  OGCM.GRIDSPEC: mit.ascii
 @MIT  OCEAN_DIR: mitocean_run
@@ -353,7 +352,7 @@ RECORD_REF_TIME: >>>REFTIME<<< >>>FCSTIME<<<
 #   REPLAY_FILE09: ana/Y%y4/M%m2/@REPLAY_ANA_EXPID.ana09.eta.%y4%m2%d2_%h2z.nc4
 #   REPLAY_FILE_FREQUENCY:       10800
 #   REPLAY_FILE_REFERENCE_TIME: 000000
- 
+
 # MERRA-2 Regular REPLAY Configuration
 # --------------------------------------------
 #M2 REPLAY_ANA_EXPID: MERRA-2
@@ -991,15 +990,15 @@ USE_WAVES: 0
 @COUPLED steady_state_ocean: 0
 @COUPLED OCEAN_PICE_SCALING: 0.0
 
-# For running MOM5 coupled model in dual ocean mode, uncomment three lines below,
+# For running MOM6 coupled model in dual ocean mode, uncomment three lines below,
 # make sure that regular replay is enabled, proper PRECIP_FILE is chosen,
 # sst.data and fraci.data are pointing to read forcing files on tripolar grid,
 # the run starts at 21z/03z/09z/15z,
 # HISTORY.rc collections have proper ref_time field
 # ---------------------------------------------------------------------------
-@MOM5#DUAL_OCEAN: 1
-@MOM5#DATA_SST_FILE: sst.data
-@MOM5#DATA_FRT_FILE: fraci.data
+@MOM6#DUAL_OCEAN: 1
+@MOM6#DATA_SST_FILE: sst.data
+@MOM6#DATA_FRT_FILE: fraci.data
 
 @COUPLED
 @COUPLED# Section for CICE
diff --git a/gcm_forecast.tmpl b/gcm_forecast.tmpl
index 6db667ca..263ff730 100755
--- a/gcm_forecast.tmpl
+++ b/gcm_forecast.tmpl
@@ -414,7 +414,6 @@ done:
 setenv BCSDIR    @BCSDIR
 @DATAOCEANsetenv SSTDIR    @SSTDIR
 setenv BCRSLV    @ATMOStag_@OCEANtag
-@MOM5setenv SSTDIR  @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}/v1
 @MOM6setenv SSTDIR  @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}/v1
 
 #this is hard-wired for NAS for now - should make it more general
@@ -690,7 +689,6 @@ endif
 
 if (! -e tile.bin) then
 $GEOSBIN/binarytile.x tile.data tile.bin
-@MOM5 $GEOSBIN/binarytile.x tile_hist.data tile_hist.bin
 endif
 
 # If running in dual ocean mode, link sst and fraci data here
diff --git a/gcm_regress.j b/gcm_regress.j
index 704a5cc1..c3d4a9aa 100755
--- a/gcm_regress.j
+++ b/gcm_regress.j
@@ -251,12 +251,6 @@ COLLECTIONS: test_collection
 @DATAOCEAN                                    'T'   , 'DYN'  ,
 @DATAOCEAN                                    'U;V' , 'DYN'  ,
 @DATAOCEAN                                    'Q'   , 'MOIST', 'QV',
-@MOM5  test_collection.fields:           'UW'   ,'MOM'  , 'US',
-@MOM5                                    'VW'   ,'MOM'  , 'VS',
-@MOM5                                    'TW'   ,'MOM'  , 'TS',
-@MOM5                                    'SW'   ,'MOM'  , 'SS',
-@MOM5                                    'SLV'  ,'MOM'  ,
-@MOM5                                    'QFLUX','OCEAN' ,
 @MOM6  test_collection.fields:           'UW'   ,'MOM6'  , 'US',
 @MOM6                                    'VW'   ,'MOM6'  , 'VS',
 @MOM6                                    'TW'   ,'MOM6'  , 'TS',
@@ -790,7 +784,6 @@ if ( $RUN_LAYOUT == TRUE) then
    @COUPLED /bin/mv AGCM.rc AGCM.tmp
    @COUPLED cat AGCM.tmp | sed -e "s?$oldstring?$newstring?g" > AGCM.rc
 
-   @MOM5sed -r -i -e "/^ *layout/ s#= ([0-9]+),*([0-9]+)#= ${test_NY},${test_NX}#" input.nml
    @MOM6sed -r -i -e "s/#override LAYOUT = 3, 2/#override LAYOUT = ${test_NY}, ${test_NX}/g" MOM_override
 
    setenv YEAR `cat cap_restart | cut -c1-4`
@@ -913,7 +906,6 @@ if ( $RUN_OPENMP == TRUE) then
    @COUPLED /bin/mv AGCM.rc AGCM.tmp
    @COUPLED cat AGCM.tmp | sed -e "s?$oldstring?$newstring?g" > AGCM.rc
 
-   @MOM5sed -r -i -e "/^ *layout/ s#= ([0-9]+),*([0-9]+)#= ${OGCM_NX0},${OGCM_NY0}#" input.nml
    @MOM6sed -r -i -e "s/#override LAYOUT = 3, 2/#override LAYOUT = ${OGCM_NX0}, ${OGCM_NY0}/g" MOM_override
 
    setenv YEAR `cat cap_restart | cut -c1-4`
diff --git a/gcm_run.j b/gcm_run.j
index ad87be4d..5da05469 100755
--- a/gcm_run.j
+++ b/gcm_run.j
@@ -369,7 +369,6 @@ done:
 setenv BCSDIR    @BCSDIR
 @DATAOCEANsetenv SSTDIR    @SSTDIR
 setenv BCRSLV    @ATMOStag_@OCEANtag
-@MOM5setenv SSTDIR  @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}/v1
 @MOM6setenv SSTDIR  @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}/v1
 
 #this is hard-wired for NAS for now - should make it more general
@@ -1322,15 +1321,7 @@ end
 
 @COUPLED # MOM-Specific Output Files
 @COUPLED # -------------------------
-@MOM5 set dsets="ocean_month"
 @MOM6 set dsets="ocean_state prog_z sfc_ave forcing"
-@MOM5  foreach dset ( $dsets )
-@MOM5  set num = `/bin/ls -1 $dset.nc | wc -l`
-@MOM5  if($num != 0) then
-@MOM5     if(! -e $EXPDIR/MOM_Output) mkdir -p $EXPDIR/MOM_Output
-@MOM5     /bin/mv $SCRDIR/$dset.nc $EXPDIR/MOM_Output/$dset.${edate}.nc
-@MOM5  endif
-@MOM5  end
 @MOM6  foreach dset ( $dsets )
 @MOM6  set num = `/bin/ls -1 $dset.nc | wc -l`
 @MOM6  if($num != 0) then
diff --git a/gcm_run.j-new_rst_approach b/gcm_run.j-new_rst_approach
index 5ae1513f..66ea81c6 100755
--- a/gcm_run.j-new_rst_approach
+++ b/gcm_run.j-new_rst_approach
@@ -310,7 +310,6 @@ done:
 setenv BCSDIR    @BCSDIR
 @DATAOCEANsetenv SSTDIR    @SSTDIR
 setenv BCRSLV    @ATMOStag_@OCEANtag
-@MOM5setenv SSTDIR  @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}/v1
 @MOM6setenv SSTDIR  @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}/v1
 
 #this is hard-wired for NAS for now - should make it more general
@@ -1328,15 +1327,7 @@ end
 
 @COUPLED # MOM-Specific Output Files
 @COUPLED # -------------------------
-@MOM5 set dsets="ocean_month"
 @MOM6 set dsets="ocean_state prog_z sfc_ave forcing"
-@MOM5  foreach dset ( $dsets )
-@MOM5  set num = `/bin/ls -1 $dset.nc | wc -l`
-@MOM5  if($num != 0) then
-@MOM5     if(! -e $EXPDIR/MOM_Output) mkdir -p $EXPDIR/MOM_Output
-@MOM5     /bin/mv $SCRDIR/$dset.nc $EXPDIR/MOM_Output/$dset.${edate}.nc
-@MOM5  endif
-@MOM5  end
 @MOM6  foreach dset ( $dsets )
 @MOM6  set num = `/bin/ls -1 $dset.nc | wc -l`
 @MOM6  if($num != 0) then
diff --git a/gcm_run_benchmark.j b/gcm_run_benchmark.j
index 8d484fdb..6d6e8f71 100755
--- a/gcm_run_benchmark.j
+++ b/gcm_run_benchmark.j
@@ -313,8 +313,6 @@ setenv CHMDIR    @CHMDIR
 setenv DATELINE  DC
 setenv EMISSIONS @EMISSIONS
 
-@MOM5setenv ABCSDIR  @COUPLEDIR/atmosphere_bcs/@LSMBCS/MOM5/@ATMOStag_@OCEANtag
-@MOM5setenv OBCSDIR  @shared_COUPLED/ocean/MOM5/${OGCM_IM}x${OGCM_JM}
 @MOM6setenv ABCSDIR  @COUPLEDIR/atmosphere_bcs/@LSMBCS/MOM6/@ATMOStag_@OCEANtag
 @MOM6setenv OBCSDIR  @shared_COUPLED/ocean/MOM6/${OGCM_IM}x${OGCM_JM}
 @COUPLEDsetenv SSTDIR  @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}
@@ -335,7 +333,6 @@ cat << _EOF_ > $FILE
 @COUPLED/bin/ln -sf $ABCSDIR/@ATMOStag_@OCEANtag-Pfafstetter.TRN   runoff.bin
 @COUPLED/bin/ln -sf $OBCSDIR/MAPL_Tripolar.nc .
 @COUPLED/bin/ln -sf $OBCSDIR/vgrid${OGCM_LM}.ascii ./vgrid.ascii
-@MOM5#/bin/ln -s @COUPLEDIR/a@HIST_IMx@HIST_JM_o${OGCM_IM}x${OGCM_JM}/DC0@HIST_IMxPC0@HIST_JM_@OCEANtag-Pfafstetter.til tile_hist.data
 @MOM6#/bin/ln -s @COUPLEDIR/MOM6/DC0@HIST_IMxPC0@HIST_JM_@OCEANtag/DC0@HIST_IMxPC0@HIST_JM_@OCEANtag-Pfafstetter.til tile_hist.data
 
 # Precip correction
@@ -725,7 +722,6 @@ endif
 
 if (! -e tile.bin) then
 $GEOSBIN/binarytile.x tile.data tile.bin
-@MOM5 $GEOSBIN/binarytile.x tile_hist.data tile_hist.bin
 endif
 
 # If running in dual ocean mode, link sst and fraci data here
@@ -1080,7 +1076,6 @@ end
 
 @COUPLED # MOM-Specific Output Files
 @COUPLED # -------------------------
-@MOM5 set dsets="ocean_month"
 @MOM6 set dsets="ocean_state prog_z sfc_ave forcing"
 @COUPLED  foreach dset ( $dsets )
 @COUPLED  set num = `/bin/ls -1 $dset.nc | wc -l`
diff --git a/gcm_setup b/gcm_setup
index bbe9e7d0..c6be3b42 100755
--- a/gcm_setup
+++ b/gcm_setup
@@ -546,7 +546,6 @@ if( $OGCM == TRUE ) then
     # -----------
     OCNMODEL:
     echo "Choose an ${C1}Ocean Model${CN}: (Default: ${C2}MOM6${CN})"
-    echo "   ${C2}MOM5${CN}"
     echo "   ${C2}MOM6${CN}"
     echo "   ${C2}MIT${CN}"
 
@@ -556,9 +555,9 @@ if( $OGCM == TRUE ) then
     else
        set OCNMODEL = `echo $OCNMODEL | tr "[:lower:]" "[:upper:]"`
 
-       if ( "$OCNMODEL" != "MOM5" & "$OCNMODEL" != "MOM6"  & "$OCNMODEL" != "MIT") then
+       if ( "$OCNMODEL" != "MOM6"  & "$OCNMODEL" != "MIT") then
           echo
-          echo "${C1}Ocean Model${CN} must be either MOM5, MOM6 or MIT!"
+          echo "${C1}Ocean Model${CN} must be either MOM6 or MIT!"
           goto OCNMODEL
        else
           echo
@@ -567,23 +566,11 @@ if( $OGCM == TRUE ) then
 
     # NOTE: We use a CMake variable here because the shared library
     # suffix is different on Linux and macOS. This is set by configure_file()
-    if ( "$OCNMODEL" == "MOM5" ) then
-       set OCEAN_NAME="MOM"
-       set OGRIDTYP  = "M5TP"
-       set OCEAN_PRELOAD = 'env @PRELOAD_COMMAND=$GEOSDIR/lib/libmom@CMAKE_SHARED_LIBRARY_SUFFIX@'
-       set MOM5=""
-       set MOM6 = "#DELETE"
-       set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM-MOM5.rc.tmpl"
-
-       set mom5_warning="######################################################\nYou (user) have chosen to set up a coupled model experiment with MOM5.\nBe aware that such a set up is _known_ to have problems. See following for more details.\nhttps://github.com/GEOS-ESM/MOM5/issues/19\nIf your intent is to help _fix_ above issue, your help is much appreciated. Thank you and good luck!\nOtherwise, until this above issue is _fixed_ you are on your own with above choice.\n######################################################"
-       echo "\033[31;5m"${mom5_warning}"\033[0m"
-       set MIT  = "#DELETE"
-    else if ( "$OCNMODEL" == "MOM6" ) then
+    if ( "$OCNMODEL" == "MOM6" ) then
        set OCEAN_NAME="MOM6"
        set OGRIDTYP  = "M6TP"
        set OCEAN_PRELOAD = 'env @PRELOAD_COMMAND=\$GEOSDIR/lib/libmom6@CMAKE_SHARED_LIBRARY_SUFFIX@'
        set MOM6=""
-       set MOM5 = "#DELETE"
        set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM.rc.tmpl"
        set MIT  = "#DELETE"
     else if ( "$OCNMODEL" == "MIT" ) then
@@ -592,7 +579,6 @@ if( $OGCM == TRUE ) then
        set OGRIDTYP  = "MITLLC"
        set MIT = ""
        set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM_MITgcm.rc.tmpl"
-       set MOM5 = "#DELETE"
        set MOM6 = "#DELETE"
     endif
 
@@ -608,25 +594,6 @@ if( $OGCM == TRUE ) then
         set OGCM_JM = 15
         set OGCM_IM = `expr $OGCM_JM \* 360`
 
-    else if ( $OCEAN_NAME == "MOM" ) then
-        set Resolution = `echo 360 200`
-        echo "Enter the Ocean Lat/Lon ${C1}Horizontal Resolution${CN}: ${C2}IM JM${CN} (Default:" $Resolution")"
-        set Resolution = `echo $<`
-        set num = $#Resolution
-        if( $num == 2 ) then
-           set OGCM_IM = $Resolution[1]
-           set OGCM_JM = $Resolution[2]
-        else
-           set Resolution = `echo 360 200`
-
-           if( $num == 0 ) then
-              set OGCM_IM = $Resolution[1]
-              set OGCM_JM = $Resolution[2]
-           else
-              goto CORSLV
-           endif
-        endif
-
     else if ( "$OCNMODEL" == "MOM6" ) then
        # For MOM6 we currently have only 3 allowed ocean resolutions based on the
        # atmospheric resolution. The allowed are:
@@ -910,7 +877,6 @@ else
     set OCEAN_PRELOAD = ""
     set OGCM_LM   =  34
     set COUPLED   = "#DELETE"
-    set MOM5      = "#DELETE"
     set MOM6      = "#DELETE"
     set CICE4     = "#DELETE"
     set CICE6     = "#DELETE"
@@ -2378,7 +2344,6 @@ s?@FORCEDAS?$FORCEDAS?g
 s?@FORCEGCM?$FORCEGCM?g
 s?@COUPLED?$COUPLED?g
 s?@CLDMICRO?$CLDMICRO?g
-s?@MOM5?$MOM5?g
 s?@MOM6?$MOM6?g
 s?@OCNMODEL?$OCNMODEL?g
 s?@CICE4?$CICE4?g
@@ -2538,11 +2503,7 @@ set FILES = `echo $FILES`
 set TMPOCEANDIR = `mktemp -d`
 
 if( $OGCM == TRUE & "$OCNMODEL" != "MIT" ) then
-   if ( $OCEAN_NAME == "MOM" ) then
-      /bin/cp ${ETCDIR}/MOM5/geos5/${OGCM_IM}x${OGCM_JM}/INPUT/input.nml ${TMPOCEANDIR}
-      /bin/cp ${ETCDIR}/MOM5/geos5/${OGCM_IM}x${OGCM_JM}/INPUT/*table ${TMPOCEANDIR}
-      set FILES = "$FILES field_table "
-   else if ( $OCEAN_NAME == "MOM6" ) then
+   if ( $OCEAN_NAME == "MOM6" ) then
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/MOM_input ${TMPOCEANDIR}
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/MOM_override ${TMPOCEANDIR}
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/input.nml ${TMPOCEANDIR}
@@ -2797,13 +2758,6 @@ if( $OGCM == TRUE ) then
 
       sed -i -e "s/DT = [0-9]*\.[0-9]*/DT = $OCEAN_DT/g" \
              -e "s/DT_THERM = [0-9]*\.[0-9]*/DT_THERM = $OCEAN_DT/g" $HOMDIR/MOM_override
-   else if ("$OCNMODEL" == "MOM5" ) then
-      # With MOM5 we need to change dt lines in input.nml to
-      # use $OCEAN_DT instead. NOTE: This sed assumes integer followed by comma
-
-      sed -i -e "s/dt_cpld = [0-9]*,/dt_cpld = $OCEAN_DT,/g" \
-             -e "s/dt_atmos = [0-9]*,/dt_atmos = $OCEAN_DT,/g" $HOMDIR/input.nml
-
    endif
 
 endif
@@ -3061,25 +3015,11 @@ if( $OGCM == TRUE ) then
 
 if ("$OCNMODEL" != "MIT" ) then
 
-# Some files are common to both MOM and MOM6
 cat >> $FILES_TO_PROCESS << EOF
 HOMDIR/input.nml
 HOMDIR/diag_table
 HOMDIR/__init__.py
 EXPDIR/plot/plotocn.j
-EOF
-endif
-
-# Some files are specific to MOM
-if ( "$OCNMODEL" == "MOM" ) then
-cat >> $FILES_TO_PROCESS << EOF
-HOMDIR/field_table
-EOF
-endif
-
-# Some files are specific to MOM6
-if ( "$OCNMODEL" == "MOM6" ) then
-cat >> $FILES_TO_PROCESS << EOF
 HOMDIR/MOM_override
 HOMDIR/MOM_input
 HOMDIR/data_table
diff --git a/geoschemchem_setup b/geoschemchem_setup
index 1894457d..4a78ef66 100755
--- a/geoschemchem_setup
+++ b/geoschemchem_setup
@@ -546,7 +546,6 @@ if( $OGCM == TRUE ) then
     # -----------
     OCNMODEL:
     echo "Choose an ${C1}Ocean Model${CN}: (Default: ${C2}MOM6${CN})"
-    echo "   ${C2}MOM5${CN}"
     echo "   ${C2}MOM6${CN}"
     echo "   ${C2}MIT${CN}"
 
@@ -556,9 +555,9 @@ if( $OGCM == TRUE ) then
     else
        set OCNMODEL = `echo $OCNMODEL | tr "[:lower:]" "[:upper:]"`
 
-       if ( "$OCNMODEL" != "MOM5" & "$OCNMODEL" != "MOM6"  & "$OCNMODEL" != "MIT") then
+       if ( "$OCNMODEL" != "MOM6"  & "$OCNMODEL" != "MIT") then
           echo
-          echo "${C1}Ocean Model${CN} must be either MOM5, MOM6 or MIT!"
+          echo "${C1}Ocean Model${CN} must be either MOM6 or MIT!"
           goto OCNMODEL
        else
           echo
@@ -567,23 +566,11 @@ if( $OGCM == TRUE ) then
 
     # NOTE: We use a CMake variable here because the shared library
     # suffix is different on Linux and macOS. This is set by configure_file()
-    if ( "$OCNMODEL" == "MOM5" ) then
-       set OCEAN_NAME="MOM"
-       set OGRIDTYP  = "M5TP"
-       set OCEAN_PRELOAD = 'env @PRELOAD_COMMAND=$GEOSDIR/lib/libmom@CMAKE_SHARED_LIBRARY_SUFFIX@'
-       set MOM5=""
-       set MOM6 = "#DELETE"
-       set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM-MOM5.rc.tmpl"
-
-       set mom5_warning="######################################################\nYou (user) have chosen to set up a coupled model experiment with MOM5.\nBe aware that such a set up is _known_ to have problems. See following for more details.\nhttps://github.com/GEOS-ESM/MOM5/issues/19\nIf your intent is to help _fix_ above issue, your help is much appreciated. Thank you and good luck!\nOtherwise, until this above issue is _fixed_ you are on your own with above choice.\n######################################################"
-       echo "\033[31;5m"${mom5_warning}"\033[0m"
-       set MIT  = "#DELETE"
-    else if ( "$OCNMODEL" == "MOM6" ) then
+    if ( "$OCNMODEL" == "MOM6" ) then
        set OCEAN_NAME="MOM6"
        set OGRIDTYP  = "M6TP"
        set OCEAN_PRELOAD = 'env @PRELOAD_COMMAND=\$GEOSDIR/lib/libmom6@CMAKE_SHARED_LIBRARY_SUFFIX@'
        set MOM6=""
-       set MOM5 = "#DELETE"
        set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM.rc.tmpl"
        set MIT  = "#DELETE"
     else if ( "$OCNMODEL" == "MIT" ) then
@@ -592,7 +579,6 @@ if( $OGCM == TRUE ) then
        set OGRIDTYP  = "MITLLC"
        set MIT = ""
        set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM_MITgcm.rc.tmpl"
-       set MOM5 = "#DELETE"
        set MOM6 = "#DELETE"
     endif
 
@@ -608,25 +594,6 @@ if( $OGCM == TRUE ) then
         set OGCM_JM = 15
         set OGCM_IM = `expr $OGCM_JM \* 360`
 
-    else if ( $OCEAN_NAME == "MOM" ) then
-        set Resolution = `echo 360 200`
-        echo "Enter the Ocean Lat/Lon ${C1}Horizontal Resolution${CN}: ${C2}IM JM${CN} (Default:" $Resolution")"
-        set Resolution = `echo $<`
-        set num = $#Resolution
-        if( $num == 2 ) then
-           set OGCM_IM = $Resolution[1]
-           set OGCM_JM = $Resolution[2]
-        else
-           set Resolution = `echo 360 200`
-
-           if( $num == 0 ) then
-              set OGCM_IM = $Resolution[1]
-              set OGCM_JM = $Resolution[2]
-           else
-              goto CORSLV
-           endif
-        endif
-
     else if ( "$OCNMODEL" == "MOM6" ) then
        # For MOM6 we currently have only 3 allowed ocean resolutions based on the
        # atmospheric resolution. The allowed are:
@@ -910,7 +877,6 @@ else
     set OCEAN_PRELOAD = ""
     set OGCM_LM   =  34
     set COUPLED   = "#DELETE"
-    set MOM5      = "#DELETE"
     set MOM6      = "#DELETE"
     set CICE4     = "#DELETE"
     set CICE6     = "#DELETE"
@@ -1438,6 +1404,7 @@ endif
 # Enter Land Surface Model Boundary Conditions
 # -----------------------------------------------------------
 LSM_BCS:
+
 # If we are running DATA_ATMOS, we can skip the Land bits, but we must still fill
 # things out with something. So we use the default Land settings.
 
@@ -1926,8 +1893,8 @@ else
               setenv    POST_T  "8:00:00"                                              # Wallclock Time   for gcm_post.j
               setenv    PLOT_T  "12:00:00"                                             # Wallclock Time   for gcm_plot.j
               setenv ARCHIVE_T  "1:00:00"                                              # Wallclock Time   for gcm_archive.j
-              setenv  RUN_Q     NULL                                                   # batch queue name for gcm_run.j
-              setenv  RUN_P     NULL                                                   # PE Configuration for gcm_run.j
+              setenv  RUN_Q     "DELETE"                                               # batch queue name for gcm_run.j
+              setenv  RUN_P   "SBATCH --ntasks=${MODEL_NPES}"                          # PE Configuration for gcm_run.j
               setenv  RUN_FP    NULL                                                   # PE Configuration for gcm_forecast.j
               setenv  REGRESS_P NULL                                                   # PE Configuration for gcm_regress.j
               setenv    POST_Q  NULL                                                   # batch queue name for gcm_post.j
@@ -1951,12 +1918,15 @@ else
               setenv WRKDIR     $HOME                                                  # user work directory
               setenv COUPLEDIR  ${BOUNDARY_DIR}/bcs_shared/make_bcs_inputs/ocean       # Coupled Ocean/Atmos Forcing
               setenv GWDRSDIR   ${BOUNDARY_DIR}/GWD_RIDGE                              # Location of GWD_RIDGE files
-              set NX = 1
-              set NY = 6
-              # By default on desktop, just ignore IOSERVER for now
-              set USE_IOSERVER = 0
-              set NUM_OSERVER_NODES = 0
-              set NUM_BACKEND_PES = 0
+endif
+
+if( $SITE == 'GMAO.desktop' ) then
+   # By default on desktop, just ignore IOSERVER for now
+   set USE_IOSERVER = 0
+   set NUM_OSERVER_NODES = 0
+   set NUM_BACKEND_PES = 0
+   set NX = 1
+   set NY = 6
 endif
 
 #######################################################################
@@ -2406,7 +2376,6 @@ s?@FORCEDAS?$FORCEDAS?g
 s?@FORCEGCM?$FORCEGCM?g
 s?@COUPLED?$COUPLED?g
 s?@CLDMICRO?$CLDMICRO?g
-s?@MOM5?$MOM5?g
 s?@MOM6?$MOM6?g
 s?@OCNMODEL?$OCNMODEL?g
 s?@CICE4?$CICE4?g
@@ -2428,10 +2397,10 @@ s?@OCEAN_NAME?$OCEAN_NAME?g
 s?@OCEAN_PRELOAD?$OCEAN_PRELOAD?g
 
 s?@4DIAUDAS?#DELETE?g
-s?@REGULAR_REPLAY?#?g
 s?@REGULAR_REPLAY_GMAO?#?g
 s?@REGULAR_REPLAY_NCEP?#DELETE?g
 s?@REGULAR_REPLAY_ECMWF?#DELETE?g
+s?@REGULAR_REPLAY?#?g
 s?ana4replay.eta.%y4%m2%d2_%h2z.nc4?/discover/nobackup/projects/gmao/merra2/data/ana/MERRA2_all/Y%y4/M%m2/MERRA2.ana.eta.%y4%m2%d2_%h2z.nc4?g
 
 s?@REPLAY_ANA_EXPID?$REPLAY_ANA_EXPID?g
@@ -2568,11 +2537,7 @@ set FILES = `echo $FILES`
 set TMPOCEANDIR = `mktemp -d`
 
 if( $OGCM == TRUE & "$OCNMODEL" != "MIT" ) then
-   if ( $OCEAN_NAME == "MOM" ) then
-      /bin/cp ${ETCDIR}/MOM5/geos5/${OGCM_IM}x${OGCM_JM}/INPUT/input.nml ${TMPOCEANDIR}
-      /bin/cp ${ETCDIR}/MOM5/geos5/${OGCM_IM}x${OGCM_JM}/INPUT/*table ${TMPOCEANDIR}
-      set FILES = "$FILES field_table "
-   else if ( $OCEAN_NAME == "MOM6" ) then
+   if ( $OCEAN_NAME == "MOM6" ) then
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/MOM_input ${TMPOCEANDIR}
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/MOM_override ${TMPOCEANDIR}
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/input.nml ${TMPOCEANDIR}
@@ -2991,13 +2956,6 @@ if( $OGCM == TRUE ) then
 
       sed -i -e "s/DT = [0-9]*\.[0-9]*/DT = $OCEAN_DT/g" \
              -e "s/DT_THERM = [0-9]*\.[0-9]*/DT_THERM = $OCEAN_DT/g" $HOMDIR/MOM_override
-   else if ("$OCNMODEL" == "MOM5" ) then
-      # With MOM5 we need to change dt lines in input.nml to
-      # use $OCEAN_DT instead. NOTE: This sed assumes integer followed by comma
-
-      sed -i -e "s/dt_cpld = [0-9]*,/dt_cpld = $OCEAN_DT,/g" \
-             -e "s/dt_atmos = [0-9]*,/dt_atmos = $OCEAN_DT,/g" $HOMDIR/input.nml
-
    endif
 
 endif
@@ -3272,25 +3230,11 @@ if( $OGCM == TRUE ) then
 
 if ("$OCNMODEL" != "MIT" ) then
 
-# Some files are common to both MOM and MOM6
 cat >> $FILES_TO_PROCESS << EOF
 HOMDIR/input.nml
 HOMDIR/diag_table
 HOMDIR/__init__.py
 EXPDIR/plot/plotocn.j
-EOF
-endif
-
-# Some files are specific to MOM
-if ( "$OCNMODEL" == "MOM" ) then
-cat >> $FILES_TO_PROCESS << EOF
-HOMDIR/field_table
-EOF
-endif
-
-# Some files are specific to MOM6
-if ( "$OCNMODEL" == "MOM6" ) then
-cat >> $FILES_TO_PROCESS << EOF
 HOMDIR/MOM_override
 HOMDIR/MOM_input
 HOMDIR/data_table
diff --git a/gmichem_setup b/gmichem_setup
index 0d36a01f..1dda87f2 100755
--- a/gmichem_setup
+++ b/gmichem_setup
@@ -546,7 +546,6 @@ if( $OGCM == TRUE ) then
     # -----------
     OCNMODEL:
     echo "Choose an ${C1}Ocean Model${CN}: (Default: ${C2}MOM6${CN})"
-    echo "   ${C2}MOM5${CN}"
     echo "   ${C2}MOM6${CN}"
     echo "   ${C2}MIT${CN}"
 
@@ -556,9 +555,9 @@ if( $OGCM == TRUE ) then
     else
        set OCNMODEL = `echo $OCNMODEL | tr "[:lower:]" "[:upper:]"`
 
-       if ( "$OCNMODEL" != "MOM5" & "$OCNMODEL" != "MOM6"  & "$OCNMODEL" != "MIT") then
+       if ( "$OCNMODEL" != "MOM6"  & "$OCNMODEL" != "MIT") then
           echo
-          echo "${C1}Ocean Model${CN} must be either MOM5, MOM6 or MIT!"
+          echo "${C1}Ocean Model${CN} must be either MOM6 or MIT!"
           goto OCNMODEL
        else
           echo
@@ -567,23 +566,11 @@ if( $OGCM == TRUE ) then
 
     # NOTE: We use a CMake variable here because the shared library
     # suffix is different on Linux and macOS. This is set by configure_file()
-    if ( "$OCNMODEL" == "MOM5" ) then
-       set OCEAN_NAME="MOM"
-       set OGRIDTYP  = "M5TP"
-       set OCEAN_PRELOAD = 'env @PRELOAD_COMMAND=$GEOSDIR/lib/libmom@CMAKE_SHARED_LIBRARY_SUFFIX@'
-       set MOM5=""
-       set MOM6 = "#DELETE"
-       set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM-MOM5.rc.tmpl"
-
-       set mom5_warning="######################################################\nYou (user) have chosen to set up a coupled model experiment with MOM5.\nBe aware that such a set up is _known_ to have problems. See following for more details.\nhttps://github.com/GEOS-ESM/MOM5/issues/19\nIf your intent is to help _fix_ above issue, your help is much appreciated. Thank you and good luck!\nOtherwise, until this above issue is _fixed_ you are on your own with above choice.\n######################################################"
-       echo "\033[31;5m"${mom5_warning}"\033[0m"
-       set MIT  = "#DELETE"
-    else if ( "$OCNMODEL" == "MOM6" ) then
+    if ( "$OCNMODEL" == "MOM6" ) then
        set OCEAN_NAME="MOM6"
        set OGRIDTYP  = "M6TP"
        set OCEAN_PRELOAD = 'env @PRELOAD_COMMAND=\$GEOSDIR/lib/libmom6@CMAKE_SHARED_LIBRARY_SUFFIX@'
        set MOM6=""
-       set MOM5 = "#DELETE"
        set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM.rc.tmpl"
        set MIT  = "#DELETE"
     else if ( "$OCNMODEL" == "MIT" ) then
@@ -592,7 +579,6 @@ if( $OGCM == TRUE ) then
        set OGRIDTYP  = "MITLLC"
        set MIT = ""
        set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM_MITgcm.rc.tmpl"
-       set MOM5 = "#DELETE"
        set MOM6 = "#DELETE"
     endif
 
@@ -608,25 +594,6 @@ if( $OGCM == TRUE ) then
         set OGCM_JM = 15
         set OGCM_IM = `expr $OGCM_JM \* 360`
 
-    else if ( $OCEAN_NAME == "MOM" ) then
-        set Resolution = `echo 360 200`
-        echo "Enter the Ocean Lat/Lon ${C1}Horizontal Resolution${CN}: ${C2}IM JM${CN} (Default:" $Resolution")"
-        set Resolution = `echo $<`
-        set num = $#Resolution
-        if( $num == 2 ) then
-           set OGCM_IM = $Resolution[1]
-           set OGCM_JM = $Resolution[2]
-        else
-           set Resolution = `echo 360 200`
-
-           if( $num == 0 ) then
-              set OGCM_IM = $Resolution[1]
-              set OGCM_JM = $Resolution[2]
-           else
-              goto CORSLV
-           endif
-        endif
-
     else if ( "$OCNMODEL" == "MOM6" ) then
        # For MOM6 we currently have only 3 allowed ocean resolutions based on the
        # atmospheric resolution. The allowed are:
@@ -999,7 +966,6 @@ else
     set OCEAN_PRELOAD = ""
     set OGCM_LM   =  34
     set COUPLED   = "#DELETE"
-    set MOM5      = "#DELETE"
     set MOM6      = "#DELETE"
     set CICE4     = "#DELETE"
     set CICE6     = "#DELETE"
@@ -2085,8 +2051,8 @@ else
               setenv    POST_T  "8:00:00"                                              # Wallclock Time   for gcm_post.j
               setenv    PLOT_T  "12:00:00"                                             # Wallclock Time   for gcm_plot.j
               setenv ARCHIVE_T  "1:00:00"                                              # Wallclock Time   for gcm_archive.j
-              setenv  RUN_Q     NULL                                                   # batch queue name for gcm_run.j
-              setenv  RUN_P     NULL                                                   # PE Configuration for gcm_run.j
+              setenv  RUN_Q     "DELETE"                                               # batch queue name for gcm_run.j
+              setenv  RUN_P   "SBATCH --ntasks=${MODEL_NPES}"                          # PE Configuration for gcm_run.j
               setenv  RUN_FP    NULL                                                   # PE Configuration for gcm_forecast.j
               setenv  REGRESS_P NULL                                                   # PE Configuration for gcm_regress.j
               setenv    POST_Q  NULL                                                   # batch queue name for gcm_post.j
@@ -2110,12 +2076,15 @@ else
               setenv WRKDIR     $HOME                                                  # user work directory
               setenv COUPLEDIR  ${BOUNDARY_DIR}/bcs_shared/make_bcs_inputs/ocean       # Coupled Ocean/Atmos Forcing
               setenv GWDRSDIR   ${BOUNDARY_DIR}/GWD_RIDGE                              # Location of GWD_RIDGE files
-              set NX = 1
-              set NY = 6
-              # By default on desktop, just ignore IOSERVER for now
-              set USE_IOSERVER = 0
-              set NUM_OSERVER_NODES = 0
-              set NUM_BACKEND_PES = 0
+endif
+
+if( $SITE == 'GMAO.desktop' ) then
+   # By default on desktop, just ignore IOSERVER for now
+   set USE_IOSERVER = 0
+   set NUM_OSERVER_NODES = 0
+   set NUM_BACKEND_PES = 0
+   set NX = 1
+   set NY = 6
 endif
 
 # If SST and SEAICE files are not in the standard location:
@@ -2571,7 +2540,6 @@ s?@FORCEDAS?$FORCEDAS?g
 s?@FORCEGCM?$FORCEGCM?g
 s?@COUPLED?$COUPLED?g
 s?@CLDMICRO?$CLDMICRO?g
-s?@MOM5?$MOM5?g
 s?@MOM6?$MOM6?g
 s?@OCNMODEL?$OCNMODEL?g
 s?@CICE4?$CICE4?g
@@ -2593,10 +2561,10 @@ s?@OCEAN_NAME?$OCEAN_NAME?g
 s?@OCEAN_PRELOAD?$OCEAN_PRELOAD?g
 
 s?@4DIAUDAS?#DELETE?g
-s?@REGULAR_REPLAY?#?g
 s?@REGULAR_REPLAY_GMAO?#?g
 s?@REGULAR_REPLAY_NCEP?#DELETE?g
 s?@REGULAR_REPLAY_ECMWF?#DELETE?g
+s?@REGULAR_REPLAY?#?g
 s?ana4replay.eta.%y4%m2%d2_%h2z.nc4?/discover/nobackup/projects/gmao/merra2/data/ana/MERRA2_all/Y%y4/M%m2/MERRA2.ana.eta.%y4%m2%d2_%h2z.nc4?g
 
 s?@REPLAY_ANA_EXPID?$REPLAY_ANA_EXPID?g
@@ -2732,11 +2700,7 @@ set FILES = `echo $FILES`
 set TMPOCEANDIR = `mktemp -d`
 
 if( $OGCM == TRUE & "$OCNMODEL" != "MIT" ) then
-   if ( $OCEAN_NAME == "MOM" ) then
-      /bin/cp ${ETCDIR}/MOM5/geos5/${OGCM_IM}x${OGCM_JM}/INPUT/input.nml ${TMPOCEANDIR}
-      /bin/cp ${ETCDIR}/MOM5/geos5/${OGCM_IM}x${OGCM_JM}/INPUT/*table ${TMPOCEANDIR}
-      set FILES = "$FILES field_table "
-   else if ( $OCEAN_NAME == "MOM6" ) then
+   if ( $OCEAN_NAME == "MOM6" ) then
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/MOM_input ${TMPOCEANDIR}
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/MOM_override ${TMPOCEANDIR}
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/input.nml ${TMPOCEANDIR}
@@ -3216,13 +3180,6 @@ if( $OGCM == TRUE ) then
 
       sed -i -e "s/DT = [0-9]*\.[0-9]*/DT = $OCEAN_DT/g" \
              -e "s/DT_THERM = [0-9]*\.[0-9]*/DT_THERM = $OCEAN_DT/g" $HOMDIR/MOM_override
-   else if ("$OCNMODEL" == "MOM5" ) then
-      # With MOM5 we need to change dt lines in input.nml to
-      # use $OCEAN_DT instead. NOTE: This sed assumes integer followed by comma
-
-      sed -i -e "s/dt_cpld = [0-9]*,/dt_cpld = $OCEAN_DT,/g" \
-             -e "s/dt_atmos = [0-9]*,/dt_atmos = $OCEAN_DT,/g" $HOMDIR/input.nml
-
    endif
 
 endif
@@ -3480,25 +3437,11 @@ if( $OGCM == TRUE ) then
 
 if ("$OCNMODEL" != "MIT" ) then
 
-# Some files are common to both MOM and MOM6
 cat >> $FILES_TO_PROCESS << EOF
 HOMDIR/input.nml
 HOMDIR/diag_table
 HOMDIR/__init__.py
 EXPDIR/plot/plotocn.j
-EOF
-endif
-
-# Some files are specific to MOM
-if ( "$OCNMODEL" == "MOM" ) then
-cat >> $FILES_TO_PROCESS << EOF
-HOMDIR/field_table
-EOF
-endif
-
-# Some files are specific to MOM6
-if ( "$OCNMODEL" == "MOM6" ) then
-cat >> $FILES_TO_PROCESS << EOF
 HOMDIR/MOM_override
 HOMDIR/MOM_input
 HOMDIR/data_table
diff --git a/linkbcs.tmpl b/linkbcs.tmpl
index 84653f75..e9416fcf 100644
--- a/linkbcs.tmpl
+++ b/linkbcs.tmpl
@@ -6,7 +6,6 @@ setenv BCSDIR    @BCSDIR
 setenv CHMDIR    @CHMDIR
 setenv BCRSLV    @ATMOStag_@OCEANtag
 
-@MOM5setenv SSTDIR  @COUPLEDIR/SST/MERRA2/@OGCM_IMx@OGCM_JM/v1
 @MOM6setenv SSTDIR  @COUPLEDIR/SST/MERRA2/@OGCM_IMx@OGCM_JM/v1
 
 @COUPLED /bin/mkdir -p RESTART
@@ -17,10 +16,8 @@ setenv BCRSLV    @ATMOStag_@OCEANtag
 @COUPLED/bin/ln -sf $CPLDIR/@OGCM_IMx@OGCM_JM/SEAWIFS_KPAR_mon_clim.@OGCM_IMx@OGCM_JM SEAWIFS_KPAR_mon_clim.data
 @COUPLED/bin/ln -sf $BCSDIR/geometry/${BCRSLV}/${BCRSLV}-Pfafstetter.til   tile.data
 @COUPLED/bin/ln -sf $BCSDIR/geometry/${BCRSLV}/${BCRSLV}-Pfafstetter.TRN   runoff.bin
-@MOM5/bin/ln -sf $CPLDIR/@OGCM_IMx@OGCM_JM/MAPL_Tripolar.nc .
 @MOM6/bin/ln -sf $CPLDIR/@OGCM_IMx@OGCM_JM/MAPL_Tripolar.nc .
 @MIT/bin/ln  -sf $BCSDIR/geometry/${BCRSLV}/mit.ascii
-@MOM5/bin/ln -sf $CPLDIR/@OGCM_IMx@OGCM_JM/vgrid@OGCM_LM.ascii ./vgrid.ascii
 @MOM6/bin/ln -sf $CPLDIR/@OGCM_IMx@OGCM_JM/vgrid@OGCM_LM.ascii ./vgrid.ascii
 @MIT/bin/ln  -sf $CPLDIR/DC0360xPC0181_LL5400x15-LL.bin DC0360xPC0181_LL5400x15-LL.bin
 
diff --git a/stratchem_setup b/stratchem_setup
index 31bec1c5..55e5203f 100755
--- a/stratchem_setup
+++ b/stratchem_setup
@@ -546,7 +546,6 @@ if( $OGCM == TRUE ) then
     # -----------
     OCNMODEL:
     echo "Choose an ${C1}Ocean Model${CN}: (Default: ${C2}MOM6${CN})"
-    echo "   ${C2}MOM5${CN}"
     echo "   ${C2}MOM6${CN}"
     echo "   ${C2}MIT${CN}"
 
@@ -556,9 +555,9 @@ if( $OGCM == TRUE ) then
     else
        set OCNMODEL = `echo $OCNMODEL | tr "[:lower:]" "[:upper:]"`
 
-       if ( "$OCNMODEL" != "MOM5" & "$OCNMODEL" != "MOM6"  & "$OCNMODEL" != "MIT") then
+       if ( "$OCNMODEL" != "MOM6"  & "$OCNMODEL" != "MIT") then
           echo
-          echo "${C1}Ocean Model${CN} must be either MOM5, MOM6 or MIT!"
+          echo "${C1}Ocean Model${CN} must be either MOM6 or MIT!"
           goto OCNMODEL
        else
           echo
@@ -567,23 +566,11 @@ if( $OGCM == TRUE ) then
 
     # NOTE: We use a CMake variable here because the shared library
     # suffix is different on Linux and macOS. This is set by configure_file()
-    if ( "$OCNMODEL" == "MOM5" ) then
-       set OCEAN_NAME="MOM"
-       set OGRIDTYP  = "M5TP"
-       set OCEAN_PRELOAD = 'env @PRELOAD_COMMAND=$GEOSDIR/lib/libmom@CMAKE_SHARED_LIBRARY_SUFFIX@'
-       set MOM5=""
-       set MOM6 = "#DELETE"
-       set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM-MOM5.rc.tmpl"
-
-       set mom5_warning="######################################################\nYou (user) have chosen to set up a coupled model experiment with MOM5.\nBe aware that such a set up is _known_ to have problems. See following for more details.\nhttps://github.com/GEOS-ESM/MOM5/issues/19\nIf your intent is to help _fix_ above issue, your help is much appreciated. Thank you and good luck!\nOtherwise, until this above issue is _fixed_ you are on your own with above choice.\n######################################################"
-       echo "\033[31;5m"${mom5_warning}"\033[0m"
-       set MIT  = "#DELETE"
-    else if ( "$OCNMODEL" == "MOM6" ) then
+    if ( "$OCNMODEL" == "MOM6" ) then
        set OCEAN_NAME="MOM6"
        set OGRIDTYP  = "M6TP"
        set OCEAN_PRELOAD = 'env @PRELOAD_COMMAND=\$GEOSDIR/lib/libmom6@CMAKE_SHARED_LIBRARY_SUFFIX@'
        set MOM6=""
-       set MOM5 = "#DELETE"
        set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM.rc.tmpl"
        set MIT  = "#DELETE"
     else if ( "$OCNMODEL" == "MIT" ) then
@@ -592,7 +579,6 @@ if( $OGCM == TRUE ) then
        set OGRIDTYP  = "MITLLC"
        set MIT = ""
        set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM_MITgcm.rc.tmpl"
-       set MOM5 = "#DELETE"
        set MOM6 = "#DELETE"
     endif
 
@@ -608,25 +594,6 @@ if( $OGCM == TRUE ) then
         set OGCM_JM = 15
         set OGCM_IM = `expr $OGCM_JM \* 360`
 
-    else if ( $OCEAN_NAME == "MOM" ) then
-        set Resolution = `echo 360 200`
-        echo "Enter the Ocean Lat/Lon ${C1}Horizontal Resolution${CN}: ${C2}IM JM${CN} (Default:" $Resolution")"
-        set Resolution = `echo $<`
-        set num = $#Resolution
-        if( $num == 2 ) then
-           set OGCM_IM = $Resolution[1]
-           set OGCM_JM = $Resolution[2]
-        else
-           set Resolution = `echo 360 200`
-
-           if( $num == 0 ) then
-              set OGCM_IM = $Resolution[1]
-              set OGCM_JM = $Resolution[2]
-           else
-              goto CORSLV
-           endif
-        endif
-
     else if ( "$OCNMODEL" == "MOM6" ) then
        # For MOM6 we currently have only 3 allowed ocean resolutions based on the
        # atmospheric resolution. The allowed are:
@@ -910,7 +877,6 @@ else
     set OCEAN_PRELOAD = ""
     set OGCM_LM   =  34
     set COUPLED   = "#DELETE"
-    set MOM5      = "#DELETE"
     set MOM6      = "#DELETE"
     set CICE4     = "#DELETE"
     set CICE6     = "#DELETE"
@@ -1912,8 +1878,8 @@ else
               setenv    POST_T  "8:00:00"                                              # Wallclock Time   for gcm_post.j
               setenv    PLOT_T  "12:00:00"                                             # Wallclock Time   for gcm_plot.j
               setenv ARCHIVE_T  "1:00:00"                                              # Wallclock Time   for gcm_archive.j
-              setenv  RUN_Q     NULL                                                   # batch queue name for gcm_run.j
-              setenv  RUN_P     NULL                                                   # PE Configuration for gcm_run.j
+              setenv  RUN_Q     "DELETE"                                               # batch queue name for gcm_run.j
+              setenv  RUN_P   "SBATCH --ntasks=${MODEL_NPES}"                          # PE Configuration for gcm_run.j
               setenv  RUN_FP    NULL                                                   # PE Configuration for gcm_forecast.j
               setenv  REGRESS_P NULL                                                   # PE Configuration for gcm_regress.j
               setenv    POST_Q  NULL                                                   # batch queue name for gcm_post.j
@@ -1937,12 +1903,15 @@ else
               setenv WRKDIR     $HOME                                                  # user work directory
               setenv COUPLEDIR  ${BOUNDARY_DIR}/bcs_shared/make_bcs_inputs/ocean       # Coupled Ocean/Atmos Forcing
               setenv GWDRSDIR   ${BOUNDARY_DIR}/GWD_RIDGE                              # Location of GWD_RIDGE files
-              set NX = 1
-              set NY = 6
-              # By default on desktop, just ignore IOSERVER for now
-              set USE_IOSERVER = 0
-              set NUM_OSERVER_NODES = 0
-              set NUM_BACKEND_PES = 0
+endif
+
+if( $SITE == 'GMAO.desktop' ) then
+   # By default on desktop, just ignore IOSERVER for now
+   set USE_IOSERVER = 0
+   set NUM_OSERVER_NODES = 0
+   set NUM_BACKEND_PES = 0
+   set NX = 1
+   set NY = 6
 endif
 
 #######################################################################
@@ -2392,7 +2361,6 @@ s?@FORCEDAS?$FORCEDAS?g
 s?@FORCEGCM?$FORCEGCM?g
 s?@COUPLED?$COUPLED?g
 s?@CLDMICRO?$CLDMICRO?g
-s?@MOM5?$MOM5?g
 s?@MOM6?$MOM6?g
 s?@OCNMODEL?$OCNMODEL?g
 s?@CICE4?$CICE4?g
@@ -2414,10 +2382,10 @@ s?@OCEAN_NAME?$OCEAN_NAME?g
 s?@OCEAN_PRELOAD?$OCEAN_PRELOAD?g
 
 s?@4DIAUDAS?#DELETE?g
-s?@REGULAR_REPLAY?#?g
 s?@REGULAR_REPLAY_GMAO?#?g
 s?@REGULAR_REPLAY_NCEP?#DELETE?g
 s?@REGULAR_REPLAY_ECMWF?#DELETE?g
+s?@REGULAR_REPLAY?#?g
 s?ana4replay.eta.%y4%m2%d2_%h2z.nc4?/discover/nobackup/projects/gmao/merra2/data/ana/MERRA2_all/Y%y4/M%m2/MERRA2.ana.eta.%y4%m2%d2_%h2z.nc4?g
 
 s?@REPLAY_ANA_EXPID?$REPLAY_ANA_EXPID?g
@@ -2553,11 +2521,7 @@ set FILES = `echo $FILES`
 set TMPOCEANDIR = `mktemp -d`
 
 if( $OGCM == TRUE & "$OCNMODEL" != "MIT" ) then
-   if ( $OCEAN_NAME == "MOM" ) then
-      /bin/cp ${ETCDIR}/MOM5/geos5/${OGCM_IM}x${OGCM_JM}/INPUT/input.nml ${TMPOCEANDIR}
-      /bin/cp ${ETCDIR}/MOM5/geos5/${OGCM_IM}x${OGCM_JM}/INPUT/*table ${TMPOCEANDIR}
-      set FILES = "$FILES field_table "
-   else if ( $OCEAN_NAME == "MOM6" ) then
+   if ( $OCEAN_NAME == "MOM6" ) then
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/MOM_input ${TMPOCEANDIR}
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/MOM_override ${TMPOCEANDIR}
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/input.nml ${TMPOCEANDIR}
@@ -2922,13 +2886,6 @@ if( $OGCM == TRUE ) then
 
       sed -i -e "s/DT = [0-9]*\.[0-9]*/DT = $OCEAN_DT/g" \
              -e "s/DT_THERM = [0-9]*\.[0-9]*/DT_THERM = $OCEAN_DT/g" $HOMDIR/MOM_override
-   else if ("$OCNMODEL" == "MOM5" ) then
-      # With MOM5 we need to change dt lines in input.nml to
-      # use $OCEAN_DT instead. NOTE: This sed assumes integer followed by comma
-
-      sed -i -e "s/dt_cpld = [0-9]*,/dt_cpld = $OCEAN_DT,/g" \
-             -e "s/dt_atmos = [0-9]*,/dt_atmos = $OCEAN_DT,/g" $HOMDIR/input.nml
-
    endif
 
 endif
@@ -3190,25 +3147,11 @@ if( $OGCM == TRUE ) then
 
 if ("$OCNMODEL" != "MIT" ) then
 
-# Some files are common to both MOM and MOM6
 cat >> $FILES_TO_PROCESS << EOF
 HOMDIR/input.nml
 HOMDIR/diag_table
 HOMDIR/__init__.py
 EXPDIR/plot/plotocn.j
-EOF
-endif
-
-# Some files are specific to MOM
-if ( "$OCNMODEL" == "MOM" ) then
-cat >> $FILES_TO_PROCESS << EOF
-HOMDIR/field_table
-EOF
-endif
-
-# Some files are specific to MOM6
-if ( "$OCNMODEL" == "MOM6" ) then
-cat >> $FILES_TO_PROCESS << EOF
 HOMDIR/MOM_override
 HOMDIR/MOM_input
 HOMDIR/data_table

From a40212cd0294adeae2bd0f2dd3162bf6c1ca4c3d Mon Sep 17 00:00:00 2001
From: Matthew Thompson <matthew.thompson@nasa.gov>
Date: Mon, 8 Sep 2025 15:00:23 -0400
Subject: [PATCH 2/3] Remove some mom5-ness

---
 set_resolution_params.csh | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/set_resolution_params.csh b/set_resolution_params.csh
index cff13365..0fdae1c5 100644
--- a/set_resolution_params.csh
+++ b/set_resolution_params.csh
@@ -100,9 +100,6 @@ if( $AGCM_IM ==  "c90" ) then
            # For MOM6 c90 means atm NXxNY = 5x36
            set  NX = 5
            set  NY = 36
-        else
-           set  NX = $OGCM_NY
-           set  NY = $OGCM_NX
         endif
         set OCEAN_DT = $DT
      else

From 26de13dadca09c583d324ca8cdbb275486ae92c5 Mon Sep 17 00:00:00 2001
From: Matthew Thompson <matthew.thompson@nasa.gov>
Date: Mon, 8 Sep 2025 15:39:51 -0400
Subject: [PATCH 3/3] remove more mom5

---
 gcm_run.j | 2 --
 1 file changed, 2 deletions(-)

diff --git a/gcm_run.j b/gcm_run.j
index 63c89d0a..3df6e75c 100755
--- a/gcm_run.j
+++ b/gcm_run.j
@@ -803,8 +803,6 @@ endif
 @COUPLEDset HEARTBEAT_DT = `grep '^\s*HEARTBEAT_DT:' CAP.rc | cut -d: -f2 | awk '{print $1}'`
 
 @COUPLED sed -i -e "s/OGCM_RUN_DT: [0-9]\+\(\.[0-9]\+\)\?/OGCM_RUN_DT: $HEARTBEAT_DT/g" AGCM.rc
-@MOM5 sed -i -e "s/dt_cpld = [0-9]\+\(\.[0-9]\+\)\?,/dt_cpld = $HEARTBEAT_DT,/g" \
-@MOM5        -e "s/dt_atmos = [0-9]\+\(\.[0-9]\+\)\?,/dt_atmos = $HEARTBEAT_DT,/g" MOM_override
 @MOM6 sed -i -e "s/DT = [0-9]\+\(\.[0-9]\+\)\?/DT = $HEARTBEAT_DT/g" \
 @MOM6        -e "s/DT_THERM = [0-9]\+\(\.[0-9]\+\)\?/DT_THERM = $HEARTBEAT_DT/g" MOM_override
 @CICE6 sed -i -E "s/^([[:space:]]*dt[[:space:]]*=[[:space:]]*)[0-9]+(\.[0-9]+)?/\1${HEARTBEAT_DT}/" ice_in