Update scripts, code, tests to fix handful of issues including parse …

…namelist checking (#215)

* scripts/code improvements for more robust and correct testing

* update tests and scripts

* update test suite to allow for longer runs for some tests

cice.setup

@@ -499,6 +499,13 @@ foreach compiler ( $ncompilers )
     set casescr = "${casedir}/casescripts"
     if !( -d ${casescr}) mkdir ${casescr}
 
+    # set default test output as failure
+    if (${docase} == 0) then
+      echo "#---" >! test_output
+      echo "FAIL ${testname_noid} build" >> test_output
+      echo "FAIL ${testname_noid} run" >> test_output
+    endif
+
     # from basic script dir to case
     foreach file (cice.build cice.settings Makefile ice_in makdep.c setup_run_dirs.csh)
       if !(-e ${ICE_SCRIPTS}/$file) then
@@ -759,6 +766,10 @@ EOF2
 
     ${casescr}/parse_settings.sh cice.settings ${fsmods}
     ${casescr}/parse_namelist.sh ice_in ${fimods}
+    if ($status != 0) then
+      echo "${0}: ERROR, parse_namelist.sh aborted"
+      exit -1
+    endif
     source ./cice.settings
     source ./env.${machcomp} -nomodules || exit 2
     ${casescr}/parse_namelist_from_env.sh ice_in
@@ -786,9 +797,9 @@ EOF2
         exit -1
       endif
 
-      # Initial test_output file
-      echo "#---" >! test_output
-      echo "PEND ${testname_noid} " >> test_output
+#      # Initial test_output file
+#      echo "#---" >! test_output
+#      echo "PEND ${testname_noid} " >> test_output
     endif
 
     #------------------------------------------------------------

cicecore/cicedynB/dynamics/ice_dyn_eap.F90

@@ -19,6 +19,7 @@ module ice_dyn_eap
 
       use ice_kinds_mod
       use ice_blocks, only: nx_block, ny_block
+      use ice_communicate, only: my_task, master_task
       use ice_domain_size, only: max_blocks, ncat
       use ice_constants, only: c0, c1, c2, c3, c12, p1, p2, p5, &
           p001, p027, p055, p111, p166, p222, p25, p333
@@ -416,7 +417,7 @@ subroutine eap (dt)
       ! stress tensor equation, total surface stress
       !-----------------------------------------------------------------
 
-         !$OMP PARALLEL DO PRIVATE(iblk,strtmp)
+         !$TCXOMP PARALLEL DO PRIVATE(iblk,strtmp)
          do iblk = 1, nblocks
 
 !      call ice_timer_start(timer_tmp1) ! dynamics
@@ -502,7 +503,7 @@ subroutine eap (dt)
             endif
 !      call ice_timer_stop(timer_tmp3) ! dynamics
          enddo
-         !$OMP END PARALLEL DO
+         !$TCXOMP END PARALLEL DO
 
          call ice_timer_start(timer_bound)
          if (maskhalo_dyn) then
@@ -1624,15 +1625,15 @@ subroutine update_stress_rdg (ksub, ndte, divu, tension, &
          gamma, alpha, x, y, dx, dy, da, &
          invdx, invdy, invda, invsin, &
          invleng, dtemp1, dtemp2, atempprime, &
-         puny, pi, pi2, piq
+         puny, pi, pi2, piq, pih
 
       real (kind=dbl_kind), parameter :: &
          kfriction = 0.45_dbl_kind
 
       character(len=*), parameter :: subname = '(update_stress_rdg)'
 
          call icepack_query_parameters(puny_out=puny, &
-            pi_out=pi, pi2_out=pi2, piq_out=piq)
+            pi_out=pi, pi2_out=pi2, piq_out=piq, pih_out=pih)
          call icepack_warnings_flush(nu_diag)
          if (icepack_warnings_aborted()) call abort_ice(error_message=subname, &
             file=__FILE__, line=__LINE__)
@@ -1649,8 +1650,12 @@ subroutine update_stress_rdg (ksub, ndte, divu, tension, &
 
          a22 = c1-a11
 
-! gamma: angle between general coordiantes and principal axis 
-         gamma = p5*atan2((c2*a12),(a11 - a22))
+! gamma: angle between general coordiantes and principal axis
+         if ((a11-a22) == c0) then
+           gamma = p5*(pih)
+         else
+           gamma = p5*atan2((c2*a12),(a11 - a22))
+         endif
 
 ! rotational tensor from general coordinates into principal axis
          Q11 = cos(gamma)
@@ -1673,7 +1678,11 @@ subroutine update_stress_rdg (ksub, ndte, divu, tension, &
          dtemp22 = p5*(divu - tension)
 
 ! alpha: angle between general coordiantes and principal axis
-         alpha = p5*atan2((c2*dtemp12),(dtemp11 - dtemp22))
+         if ((dtemp11-dtemp22) == c0) then
+           alpha = p5*(pih)
+         else
+           alpha = p5*atan2((c2*dtemp12),(dtemp11 - dtemp22))
+         endif
 
 ! y: angle between major principal axis of strain rate and structure tensor
 ! to make sure y between 0 and pi/2
@@ -1699,7 +1708,11 @@ subroutine update_stress_rdg (ksub, ndte, divu, tension, &
            invleng = c1/sqrt(dtemp1*dtemp1 + dtemp2*dtemp2)
            dtemp1 = dtemp1*invleng
            dtemp2 = dtemp2*invleng
-           x = atan2(dtemp2,dtemp1)
+           if ((dtemp1) == c0) then
+             x = (pih)
+           else
+             x = atan2(dtemp2,dtemp1)
+           endif
          endif
 
 !echmod to ensure the angle lies between pi/4 and 9 pi/4 
@@ -1928,7 +1941,7 @@ subroutine calc_ffrac (blockno, stressp, stressm, &
 
       real (kind=dbl_kind) :: &
          sigma11, sigma12, sigma22, &
-         gamma, sigma_1, sigma_2, &
+         gamma, sigma_1, sigma_2, pih, &
          Q11, Q12, Q11Q11, Q11Q12, Q12Q12
 
       real (kind=dbl_kind), parameter :: &
@@ -1937,11 +1950,20 @@ subroutine calc_ffrac (blockno, stressp, stressm, &
 
       character(len=*), parameter :: subname = '(calc_ffrac)'
 
+       call icepack_query_parameters(pih_out=pih)
+       call icepack_warnings_flush(nu_diag)
+       if (icepack_warnings_aborted()) call abort_ice(error_message=subname, &
+          file=__FILE__, line=__LINE__)
+
        sigma11 = p5*(stressp+stressm) 
        sigma12 = stress12 
        sigma22 = p5*(stressp-stressm) 
 
-       gamma = p5*atan2((c2*sigma12),(sigma11-sigma22))
+       if ((sigma11-sigma22) == c0) then
+         gamma = p5*(pih)
+       else
+         gamma = p5*atan2((c2*sigma12),(sigma11-sigma22))
+       endif
 
 ! rotate tensor to get into sigma principal axis
 
@@ -2023,7 +2045,6 @@ subroutine read_restart_eap()
 
       use ice_blocks, only: nghost
       use ice_boundary, only: ice_HaloUpdate_stress
-      use ice_communicate, only: my_task, master_task
       use ice_constants, only:  &
           field_loc_center, field_type_scalar
       use ice_domain, only: nblocks, halo_info

cicecore/cicedynB/dynamics/ice_dyn_evp.F90

@@ -353,7 +353,7 @@ subroutine evp (dt)
       ! stress tensor equation, total surface stress
       !-----------------------------------------------------------------
 
-         !$OMP PARALLEL DO PRIVATE(iblk,strtmp)
+         !$TCXOMP PARALLEL DO PRIVATE(iblk,strtmp)
          do iblk = 1, nblocks
 
 !            if (trim(yield_curve) == 'ellipse') then
@@ -403,7 +403,7 @@ subroutine evp (dt)
             fld2(:,:,1,iblk) = uvel(:,:,iblk)
             fld2(:,:,2,iblk) = vvel(:,:,iblk)
          enddo
-         !$OMP END PARALLEL DO
+         !$TCXOMP END PARALLEL DO
 
          call ice_timer_start(timer_bound)
          if (maskhalo_dyn) then

cicecore/cicedynB/infrastructure/ice_restart_driver.F90

@@ -481,7 +481,7 @@ subroutine restartfile (ice_ic)
       ! compute aggregate ice state and open water area
       !-----------------------------------------------------------------
 
-      !$OMP PARALLEL DO PRIVATE(iblk)
+      !$OMP PARALLEL DO PRIVATE(iblk,i,j)
       do iblk = 1, nblocks
 
       do j = 1, ny_block

cicecore/shared/ice_distribution.F90

@@ -698,6 +698,14 @@ function create_distrb_cart(nprocs, workPerBlock) result(newDistrb)
       end do
       end do
 
+   else
+      allocate (newDistrb%blockGlobalID(newDistrb%numLocalBlocks), &
+                stat=istat)
+      if (istat > 0) then
+         call abort_ice( &
+            'create_distrb_cart: error allocating blockGlobalID')
+         return
+      endif
    endif
 
 !----------------------------------------------------------------------

configuration/scripts/cice.build

@@ -7,7 +7,7 @@
 set ciceexe = "UnDEFineD"
 if ($#argv == 1) then
   set ciceexe = $1
-  echo "${0}: tcx ciceexe = ${ciceexe}"
+  echo "${0}: ciceexe = ${ciceexe}"
   if (-e ${ciceexe}) then
 
     source ./cice.settings

configuration/scripts/ice_in

@@ -171,11 +171,11 @@
     fe_data_type    = 'default'
     fyear_init      = 1997
     ycycle          = 1
-    atm_data_dir    = '/glade/u/home/tcraig/cice_data/'
-    ocn_data_dir    = '/unknown_ocn_data_dir'
-    bgc_data_dir    = '/uknown_bgc_data_dir'
     atm_data_format = 'bin'
+    atm_data_dir    = '/glade/u/home/tcraig/cice_data/'
+    bgc_data_dir    = 'unknown_bgc_data_dir'
     ocn_data_format = 'bin'
+    ocn_data_dir    = '/unknown_ocn_data_dir'
     oceanmixed_file = 'unknown_oceanmixed_file'
 /
 

configuration/scripts/machines/env.hobart_intel

@@ -21,6 +21,7 @@ setenv ICE_MACHINE_WKDIR /scratch/cluster/$user/CICE_RUNS
 setenv ICE_MACHINE_INPUTDATA /fs/cgd/csm/inputdata
 setenv ICE_MACHINE_BASELINE /scratch/cluster/$user/CICE_BASELINE
 setenv ICE_MACHINE_SUBMIT "qsub"
+setenv ICE_MACHINE_QSTAT "qstat "
 setenv ICE_MACHINE_QUEUE "short"
 setenv ICE_MACHINE_ACCT P00000000
 setenv ICE_MACHINE_TPNODE 24

configuration/scripts/machines/env.hobart_nag

@@ -21,6 +21,7 @@ setenv ICE_MACHINE_WKDIR /scratch/cluster/$user/CICE_RUNS
 setenv ICE_MACHINE_INPUTDATA /fs/cgd/csm/inputdata
 setenv ICE_MACHINE_BASELINE /scratch/cluster/$user/CICE_BASELINE
 setenv ICE_MACHINE_SUBMIT "qsub"
+setenv ICE_MACHINE_QSTAT "qstat "
 setenv ICE_MACHINE_QUEUE "short"
 setenv ICE_MACHINE_ACCT P00000000
 setenv ICE_MACHINE_TPNODE 24

configuration/scripts/options/set_nml.alt01

@@ -19,7 +19,7 @@ basalstress = .true.
 shortwave = 'ccsm3'
 albedo_type = 'constant'
 formdrag = .true.
-calc_tsfc = .true.
+calc_Tsfc = .true.
 atm_data_type = 'default'
 highfreq = .true.
 fbot_xfer_type = 'Cdn_ocn'

configuration/scripts/options/set_nml.alt02

@@ -18,6 +18,6 @@ krdg_partic = 0
 krdg_redist = 0
 shortwave       = 'ccsm3'
 albedo_type     = 'ccsm3'
-calc_tsfc = .true.
+calc_Tsfc = .true.
 
 

configuration/scripts/options/set_nml.gx1

@@ -13,8 +13,7 @@ ycycle          = 1
 atm_data_format = 'bin'
 atm_data_type   = 'LYq'
 atm_data_dir    = 'ICE_MACHINE_INPUTDATA/CICE_data/forcing/gx1/COREII'
-precip_unit = 'mm_per_sec'
-ocn_data_format = 'nc'
-ocn_data_type = 'ncar'
-ocn_data_dir = 'oceanmixed_ice_depth.nc'
+precip_units    = 'mm_per_sec'
+ocn_data_dir    = 'ICE_MACHINE_INPUTDATA/CICE_data/forcing/gx1/COREII'
+bgc_data_dir    = 'ICE_MACHINE_INPUTDATA/CICE_data/forcing/gx1/WOA/MONTHLY'
 

configuration/scripts/parse_namelist.sh

@@ -10,6 +10,7 @@ filemods=$2
 
 #echo "$0 $1 $2" 
 echo "running parse_namelist.sh"
+foundstring="FoundSTRING"
 
 while read -r line
 do
@@ -24,10 +25,20 @@ do
 #    echo "$line $vname $value"
 
     #sed -i 's|\(^\s*'"$vname"'\s*\=\s*\)\(.*$\)|\1'"$value"'|g' $filename
-    sed -i.sedbak -e 's|\(^[[:space:]]*'"$vname"'[[:space:]]*=[[:space:]]*\)\(.*$\)|\1'"$value"'|g' $filename
-    if [[ -e "${filename}.sedbak" ]]; then
-      rm ${filename}.sedbak
+    cp ${filename} ${filename}.check
+    sed -i -e 's|\(^[[:space:]]*'"$vname"'[[:space:]]*=[[:space:]]*\)\(.*$\)|\1'"$foundstring"'|g' ${filename}.check
+    grep -q ${foundstring} ${filename}.check
+    if [ $? -eq 0 ]; then
+      sed -i.sedbak -e 's|\(^[[:space:]]*'"$vname"'[[:space:]]*=[[:space:]]*\)\(.*$\)|\1'"$value"'|g' ${filename}
+      if [[ -e "${filename}.sedbak" ]]; then
+        rm ${filename}.sedbak
+      fi
+    else
+      echo "$0 ERROR: parsing error for ${vname}"
+      exit -99
     fi
+    rm ${filename}.check
+
   fi
 
 done < "$filemods"

configuration/scripts/tests/base_suite.ts

@@ -8,8 +8,8 @@ smoke          gx3     8x2        diag24,run1year,medium
 decomp         gx3     4x2x25x29x5
 smoke          gx3     4x2        diag1,run5day          smoke_gx3_8x2_diag1_run5day
 smoke          gx3     4x1        diag1,run5day,thread   smoke_gx3_8x2_diag1_run5day
-restart        gx1     40x4       droundrobin,short
-restart        tx1     40x4       dsectrobin,short
+restart        gx1     40x4       droundrobin,medium
+restart        tx1     40x4       dsectrobin,medium
 restart        gx3     4x4        none
 restart        gx3     4x4        iobinary
 restart        gx3     6x2        alt01
@@ -19,5 +19,5 @@ restart        gx3     4x4        alt04
 restart        gx3     4x4        alt05
 restart        gbox128  4x2       none
 restart        gbox128  4x2       boxdyn
-restart        gbox128  2x2       boxadv
+restart        gbox128  2x2       boxadv,short
 restart        gbox128  4x4       boxrestore

configuration/scripts/tests/decomp_suite.ts

@@ -6,7 +6,7 @@ restart        gx3     6x2x4x29x18   dspacecurve        restart_gx3_4x2x25x29x4_
 restart        gx3     8x2x8x10x20   droundrobin        restart_gx3_4x2x25x29x4_dslenderX2
 restart        gx3     6x2x50x58x1   droundrobin        restart_gx3_4x2x25x29x4_dslenderX2
 restart        gx3     4x2x19x19x10  droundrobin        restart_gx3_4x2x25x29x4_dslenderX2
-restart        gx3     1x20x5x29x80  dsectrobin         restart_gx3_4x2x25x29x4_dslenderX2
+restart        gx3     1x20x5x29x80  dsectrobin,short   restart_gx3_4x2x25x29x4_dslenderX2
 restart        gx3     16x2x5x10x20  drakeX2            restart_gx3_4x2x25x29x4_dslenderX2
 restart        gx3     8x2x8x10x20   droundrobin,maskhalo   restart_gx3_4x2x25x29x4_dslenderX2
 restart        gx3     1x4x25x29x16  droundrobin        restart_gx3_4x2x25x29x4_dslenderX2

configuration/scripts/tests/poll_queue.csh

@@ -16,6 +16,9 @@ foreach line ( "`cat suite.log`" )
     if ( "$line" =~ *'COMPILE SUCCESSFUL'* ) then
       set job_id = 1
     endif
+    if ( "$line" =~ *'ciceexe'* ) then
+      set job_id = 1
+    endif
   endif
 end