Some cesm build changes

cime_config/buildlib

@@ -56,7 +56,7 @@ def _main_func():
         complib = os.path.join(libroot,"librof.a")
         makefile = os.path.join(casetools, "Makefile")
 
-        cmd = "{} complib -j {} MODEL=mizuRoute COMPLIB={} -f {} {}" \
+        cmd = "{} complib -j {} COMP_NAME=mizuRoute COMPLIB={} -f {} {}" \
               .format(gmake, gmake_j, complib, makefile, get_standard_makefile_args(case))
 
         rc, out, err = run_cmd(cmd)

cime_config/buildnml

@@ -52,6 +52,10 @@ def _create_control_files(case, caseroot, srcroot, confdir, inst_string, infile,
     logger.debug("  mizuRoute lnd grid is %s ", config['lnd_grid'])
     logger.debug("  mizuRoute rof grid is %s ", config['rof_grid'])
     #----------------------------------------------------
+    # Create dictionary of files that will be read in
+    #----------------------------------------------------
+    files = {}
+    #----------------------------------------------------
     # Settings that depend on the resolution
     #----------------------------------------------------
     if (    config['rof_grid'] == "HDMAmz" ):
@@ -175,6 +179,8 @@ def _create_control_files(case, caseroot, srcroot, confdir, inst_string, infile,
     ctl.set( "varname_downSegId", varname_downSegId )
     ctl.set( "varname_pfafCode", varname_pfafCode )
 
+    files['fname_ntopold'] = os.path.join( ctl.get('ancil_dir'), ctl.get('fname_ntopOld') )
+
     #----------------------------------------------------
     # Set the restart file depending on start type
     #----------------------------------------------------
@@ -189,6 +195,7 @@ def _create_control_files(case, caseroot, srcroot, confdir, inst_string, infile,
             filename = "%s.mizuRoute.r.%s-%s.nc" %(run_refcase, run_refdate, run_tod)
 
         ctl.set( "fname_state_in", filename )
+        files['fname_state_in'] = ctl.get('fname_state_in')
 
     elif fname_state_in.strip() == '':
         fname_state_in = "empty"
@@ -215,15 +222,23 @@ def _create_control_files(case, caseroot, srcroot, confdir, inst_string, infile,
     #----------------------------------------------------
     control_file = os.path.join(confdir, "mizuRoute.control")
     nml_file = os.path.join(confdir, "mizuRoute_in")
-    write_nml_in_file(case, nmlgen, confdir, nml_file)
+    write_nml_in_file(case, nmlgen, confdir, nml_file, data_list_path)
     ctl.write( control_file )
+    #----------------------------------------------------
+    # Append list of files needed to file list file
+    #----------------------------------------------------
+    print( data_list_path )
+    fileslist = open( data_list_path, "a" )
+    print( files )
+    for datafile in files:
+       print( datafile )
+       fileslist.write( datafile + " = " + files[datafile] + "\n" )
+
+    fileslist.close()
 
 ###############################################################################
-def write_nml_in_file(case, nmlgen, confdir, nml_file):
+def write_nml_in_file(case, nmlgen, confdir, nml_file, data_list_path):
 ###############################################################################
-    data_list_path = os.path.join(case.get_case_root(), "Buildconf", "rof.input_data_list")
-    if os.path.exists(data_list_path):
-        os.remove(data_list_path)
     namelist_file = os.path.join(confdir, nml_file)
     nmlgen.write_output_file(namelist_file, data_list_path )
 

cime_config/testdefs/ExpectedTestFails.xml

@@ -39,7 +39,7 @@
   <test name="SMS_D.nldas2_rUSGS_mnldas2.I2000Clm50SpMizGs.cheyenne_intel.mizuroute-default">
     <phase name="RUN">
       <status>FAIL</status>
-      <issue>ESMCI/cime#143</issue>
+      <issue>#273</issue>
     </phase>
   </test>
   <test name="SMS.f19_f19_mg17_rMERIT.I2000Clm50SpMizGs.cheyenne_gnu.mizuroute-default">

cime_config/testdefs/testlist_mizuRoute.xml

@@ -13,6 +13,7 @@
    <!-- NOTE: ERP tests are known NOT to work since the MPI task count must remain the same on restart -->
    <!--       ERP tests with only threads can work hoeever -->
    <!--       PEM tests seem to need to be at least 10 days in length (see #239) -->
+   <!--       USFS grid fails currently (see #273) -->
    <!-- MPI: mpi-serial and regular as well as some threaded -->
    <!-- Short tests: minimum 1-day    Longer tests: a year to two, good to do past year boundary -->
    <!-- compsets: I2000Clm50SpMizGs -->
@@ -116,19 +117,7 @@
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Smoke test on CONUS regional grid with DEBUG on</option>
-    </options>
-  </test>
-  <test name="ERS" grid="nldas2_rUSGS_mnldas2" compset="I2000Clm50SpMizGs" testmods="mizuroute/default">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="mizu"></machine>
-      <machine name="cheyenne" compiler="gnu"   category="mizu"></machine>
-      <machine name="izumi"    compiler="intel" category="mizu"></machine>
-      <machine name="izumi"    compiler="nag"   category="mizu"></machine>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Exact restart test on CONUS regional grid with DEBUG off</option>
+      <option name="comment"  >Smoke test on CONUS regional grid with DEBUG on (only one test since this fails)</option>
     </options>
   </test>
   <test name="ERI" grid="nldas2_rHDMA_mnldas2" compset="I2000Clm50SpMizGs" testmods="mizuroute/default">

route/build/cpl/RtmTimeManager.F90

@@ -82,7 +82,9 @@ SUBROUTINE init_time(ierr, message)
     case('hours','hour','hr','h');      secPerTime=3600._r8;  timePerDay=24._r8
     case('days','day','d');             secPerTime=86400._r8; timePerDay=1._r8
     case default
-      ierr=20; message=trim(message)//'<time_units>= '//trim(time_units)//': <time_units> must be seconds, minutes, hours or days.'; return
+      ierr=20
+      message=trim(message)//'<time_units>= '//trim(time_units)//': <time_units> must be seconds, minutes, hours or days.'
+      return
   end select
 
   dt_day = dt/secprday  ! dt [sec] -> dt_day
@@ -122,7 +124,11 @@ SUBROUTINE init_time(ierr, message)
   end if
 
   ! check that the dates are aligned
-  if(endDatetime < begDatetime) then; ierr=20; message=trim(message)//'simulation end is before simulation start'; return; endif
+  if(endDatetime < begDatetime) then
+     ierr=20
+     message=trim(message)//'simulation end is before simulation start'
+     return
+  endif
 
   ! initialize model time at first time step (1) and previous time step (0)
   iTime = 1
@@ -132,8 +138,10 @@ SUBROUTINE init_time(ierr, message)
   if (masterproc .and. debug_write) then
     write(iulog,*) 'simStart datetime     = ', trim(simStart)
     write(iulog,*) 'simEnd   datetime     = ', trim(simEnd)
-    write(iulog,*) 'reference datetime    = ', refDatetime%year(), refDatetime%month(), refDatetime%day(), refDatetime%hour(), refDatetime%minute(), refDatetime%sec()
-    write(iulog,*) 'simDatetime           = ', simDatetime(1)%year(), simDatetime(1)%month(), simDatetime(1)%day(), simDatetime(1)%hour(), simDatetime(1)%minute(), simDatetime(1)%sec()
+    write(iulog,*) 'reference datetime    = ', refDatetime%year(), refDatetime%month(), refDatetime%day() &
+                                             , refDatetime%hour(), refDatetime%minute(), refDatetime%sec()
+    write(iulog,*) 'simDatetime           = ', simDatetime(1)%year(), simDatetime(1)%month(), simDatetime(1)%day() &
+                                             , simDatetime(1)%hour(), simDatetime(1)%minute(), simDatetime(1)%sec()
     write(iulog,*) 'dt [sec]              = ', dt
     write(iulog,*) 'nTime                 = ', nTime
     write(iulog,*) 'iTime, timeVar(iTime) = ', iTime, timeVar(iTime)
@@ -158,7 +166,7 @@ SUBROUTINE shr_timeStr(esmfTime, timeStr)
 
    call ESMF_TimeGet(esmfTime , yy=yy, mm=mm, dd=dd, h=hr, m=mn, s=sec, rc=rc )
 
-   write(timeStr,'(i4.4,a,i2.2,a,i2.2,a,i2.2,a,i2.2,a,i2.2)'), yy,'-',mm,'-',dd,' ',hr,':',mn,':',sec
+   write(timeStr,'(i4.4,a,i2.2,a,i2.2,a,i2.2,a,i2.2,a,i2.2)') yy,'-',mm,'-',dd,' ',hr,':',mn,':',sec
 
  END SUBROUTINE shr_timeStr
 

route/build/src/accum_runoff.f90

@@ -164,13 +164,13 @@ SUBROUTINE accum_qupstream(iEns,       &    ! input: index of runoff ensemble to
    write(fmt1,'(A,I5,A)') '(A,1X',nUps,'(1X,I10))'
    write(fmt2,'(A,I5,A)') '(A,1X',nUps,'(1X,F20.7))'
    write(*,'(2a)') new_line('a'),'** Check upstream discharge accumulation **'
-   write(*,'(a,x,I10,x,I10)') ' Reach index & ID =', segIndex, NETOPO_in(segIndex)%REACHID
+   write(*,'(a,1x,I10,1x,I10)') ' Reach index & ID =', segIndex, NETOPO_in(segIndex)%REACHID
    write(*,'(a)')             ' * upstream reach index (NETOPO_in%UREACH) and discharge (uprflux) [m3/s] :'
    write(*,fmt1)              ' UREACHK =', (NETOPO_in(segIndex)%UREACHK(iUps), iUps=1,nUps)
    write(*,fmt2)              ' prflux  =', (RCHFLX_out(iens,NETOPO_in(segIndex)%UREACHI(iUps))%ROUTE(idxSUM)%REACH_Q, iUps=1,nUps)
    write(*,'(a)')             ' * local area discharge (RCHFLX_out%BASIN_QR(1)) and final discharge (RCHFLX_out%ROUTE(idxSUM)%REACH_Q) [m3/s] :'
-   write(*,'(a,x,F15.7)')     ' RCHFLX_out%BASIN_QR(1) =', RCHFLX_out(iEns,segIndex)%BASIN_QR(1)
-   write(*,'(a,x,F15.7)')     ' RCHFLX_out%ROUTE(idxSUM)%REACH_Q =', RCHFLX_out(iens,segIndex)%ROUTE(idxSUM)%REACH_Q
+   write(*,'(a,1x,F15.7)')     ' RCHFLX_out%BASIN_QR(1) =', RCHFLX_out(iEns,segIndex)%BASIN_QR(1)
+   write(*,'(a,1x,F15.7)')     ' RCHFLX_out%ROUTE(idxSUM)%REACH_Q =', RCHFLX_out(iens,segIndex)%ROUTE(idxSUM)%REACH_Q
  endif
 
  END SUBROUTINE accum_qupstream

route/build/src/dfw_route.f90

@@ -192,10 +192,10 @@ SUBROUTINE dfw_rch(iEns, segIndex, & ! input: index of runoff ensemble to be pro
    if (nUps>0) then
      do iUps = 1,nUps
        iRch_ups = NETOPO_in(segIndex)%UREACHI(iUps)      !  index of upstream of segIndex-th reach
-       write(iulog,'(A,X,I12,X,G15.4)') ' UREACHK, uprflux=',NETOPO_in(segIndex)%UREACHK(iUps),RCHFLX_out(iens, iRch_ups)%ROUTE(idxDW)%REACH_Q
+       write(iulog,'(A,1X,I12,1X,G15.4)') ' UREACHK, uprflux=',NETOPO_in(segIndex)%UREACHK(iUps),RCHFLX_out(iens, iRch_ups)%ROUTE(idxDW)%REACH_Q
      enddo
    end if
-   write(iulog,'(A,X,G15.4)') ' RCHFLX_out(iEns,segIndex)%BASIN_QR(1)=',RCHFLX_out(iEns,segIndex)%BASIN_QR(1)
+   write(iulog,'(A,1X,G15.4)') ' RCHFLX_out(iEns,segIndex)%BASIN_QR(1)=',RCHFLX_out(iEns,segIndex)%BASIN_QR(1)
  endif
 
  ! solve diffusive wave equation
@@ -208,12 +208,12 @@ SUBROUTINE dfw_rch(iEns, segIndex, & ! input: index of runoff ensemble to be pro
                      doCheck,                                 &  ! input: reach index to be examined
                      ierr, cmessage)                             ! output: error control
  if(ierr/=0)then
-    write(message, '(A,X,I12,X,A)') trim(message)//'/segment=', NETOPO_in(segIndex)%REACHID, '/'//trim(cmessage)
+    write(message, '(A,1X,I12,1X,A)') trim(message)//'/segment=', NETOPO_in(segIndex)%REACHID, '/'//trim(cmessage)
     return
  endif
 
  if(doCheck)then
-   write(iulog,'(A,X,G15.4)') ' RCHFLX_out(iens,segIndex)%REACH_Q=', RCHFLX_out(iens,segIndex)%ROUTE(idxDW)%REACH_Q
+   write(iulog,'(A,1X,G15.4)') ' RCHFLX_out(iens,segIndex)%REACH_Q=', RCHFLX_out(iens,segIndex)%ROUTE(idxDW)%REACH_Q
  endif
 
  END SUBROUTINE dfw_rch
@@ -333,14 +333,14 @@ SUBROUTINE diffusive_wave(rch_param,     & ! input: river parameter data structu
    dt = T1-T0
 
    if (doCheck) then
-     write(iulog,'(4(A,X,G15.4))') ' length [m] =',rch_param%RLENGTH,'slope [-] =',rch_param%R_SLOPE,'channel width [m] =',rch_param%R_WIDTH,'manning coef =',rch_param%R_MAN_N
+     write(iulog,'(4(A,1X,G15.4))') ' length [m] =',rch_param%RLENGTH,'slope [-] =',rch_param%R_SLOPE,'channel width [m] =',rch_param%R_WIDTH,'manning coef =',rch_param%R_MAN_N
    end if
 
    ! time-step adjustment so Courant number is less than 1
    dTsub = dt/ntSub
 
    if (doCheck) then
-     write(iulog,'(A,X,I3,A,X,G12.5)') ' No. sub timestep=',nTsub,' sub time-step [sec]=',dTsub
+     write(iulog,'(A,1X,I3,A,1X,G12.5)') ' No. sub timestep=',nTsub,' sub time-step [sec]=',dTsub
    end if
 
    allocate(Qlocal(1:nMolecule%DW_ROUTE, 0:1), stat=ierr, errmsg=cmessage)
@@ -453,7 +453,7 @@ SUBROUTINE diffusive_wave(rch_param,     & ! input: river parameter data structu
  endif
 
  if (doCheck) then
-   write(iulog,'(A,X,G12.5)') ' Qout(t) =', rflux%ROUTE(idxDW)%REACH_Q
+   write(iulog,'(A,1X,G12.5)') ' Qout(t) =', rflux%ROUTE(idxDW)%REACH_Q
  endif
 
  END SUBROUTINE diffusive_wave

route/build/src/domain_decomposition.f90

@@ -115,11 +115,11 @@ SUBROUTINE print_screen()
       associate (segIndexSub => domains_mpi(ix)%segIndex, nSubSeg => size(domains_mpi(ix)%segIndex))
       do iSeg = 1,size(segIndexSub)
        if (downIndex(segIndexSub(iSeg)) > 0) then
-       write(iulog, "(I9,x,I12,x,I9,x,I12,x,I5,x,I3)") segIndexSub(iSeg),segId(segIndexSub(iSeg)), &
+       write(iulog, "(I9,1x,I12,1x,I9,1x,I12,1x,I5,1x,I3)") segIndexSub(iSeg),segId(segIndexSub(iSeg)), &
                                                   downIndex(segIndexSub(iSeg)),segId(downIndex(segIndexSub(iSeg))), &
                                                   ix, domains_mpi(ix)%idNode
        else
-       write(iulog, "(I9,x,I12,x,I9,x,I12,x,I5,x,I3)") segIndexSub(iSeg),segId(segIndexSub(iSeg)), &
+       write(iulog, "(I9,1x,I12,1x,I9,1x,I12,1x,I5,1x,I3)") segIndexSub(iSeg),segId(segIndexSub(iSeg)), &
                                                   downIndex(segIndexSub(iSeg)),-999, &
                                                   ix, domains_mpi(ix)%idNode
        endif

route/build/src/init_model_data.f90

@@ -509,6 +509,7 @@ SUBROUTINE init_ntopo(nHRU_out, nRch_out,
   USE process_ntopo,        ONLY: check_river_properties   ! check if river network data is physically valid
   USE ncio_utils,           ONLY: get_var_dims
   USE process_ntopo,        ONLY: augment_ntopo            ! compute all the additional network topology (only compute option = on)
+  USE shr_sys_mod,          ONLY: shr_sys_system           ! share system call
 
   implicit none
   ! input: None
@@ -597,7 +598,8 @@ SUBROUTINE init_ntopo(nHRU_out, nRch_out,
     !        --> users can modify the hard-coded parameter "maxUpstreamFile" if desired
     if(tot_upstream > maxUpstreamFile) tot_upstream=0
 
-    call system('rm -f '//trim(ancil_dir)//trim(fname_ntopNew))
+    call shr_sys_system('rm -f '//trim(ancil_dir)//trim(fname_ntopNew), ierr)
+    if(ierr/=0)then; message=trim(message)//' problem deleting fname_ntopNew'; return; endif
 
     call writeData(&
                    ! input

route/build/src/irf_route.f90

@@ -222,12 +222,12 @@ subroutine segment_irf(iEns,         & ! input: index of runoff ensemble to be p
     ntdh = size(NETOPO_in(segIndex)%UH)
     write(fmt1,'(A,I5,A)') '(A, 1X',ntdh,'(1X,F20.7))'
     write(*,'(2a)') new_line('a'),'** Check Impulse Response Function routing **'
-    write(*,'(a,x,I10,x,I10)') ' Reach index & ID       =', segIndex, NETOPO_in(segIndex)%REACHID
+    write(*,'(a,1x,I10,1x,I10)') ' Reach index & ID       =', segIndex, NETOPO_in(segIndex)%REACHID
     write(*,fmt1)              ' Unit-Hydrograph        =', (NETOPO_in(segIndex)%UH(itdh), itdh=1,ntdh)
     write(*,'(a)')             ' * total discharge from upstream(q_upstream) [m3/s], local area discharge [m3/s], and Final discharge [m3/s]:'
-    write(*,'(a,x,F15.7)')     ' q_upstream             =', q_upstream
-    write(*,'(a,x,F15.7)')     ' RCHFLX_out%BASIN_QR(1) =', RCHFLX_out(iens,segIndex)%BASIN_QR(1)
-    write(*,'(a,x,F15.7)')     ' RCHFLX_out%REACH_Q =', RCHFLX_out(iens,segIndex)%ROUTE(idxIRF)%REACH_Q
+    write(*,'(a,1x,F15.7)')     ' q_upstream             =', q_upstream
+    write(*,'(a,1x,F15.7)')     ' RCHFLX_out%BASIN_QR(1) =', RCHFLX_out(iens,segIndex)%BASIN_QR(1)
+    write(*,'(a,1x,F15.7)')     ' RCHFLX_out%REACH_Q =', RCHFLX_out(iens,segIndex)%ROUTE(idxIRF)%REACH_Q
   endif
 
  end subroutine segment_irf

route/build/src/kwe_route.f90

@@ -192,10 +192,10 @@ SUBROUTINE kw_rch(iEns, segIndex, & ! input: index of runoff ensemble to be proc
    if (nUps>0) then
      do iUps = 1,nUps
        iRch_ups = NETOPO_in(segIndex)%UREACHI(iUps)      !  index of upstream of segIndex-th reach
-       write(iulog,'(A,X,I12,X,G15.4)') ' UREACHK, uprflux=',NETOPO_in(segIndex)%UREACHK(iUps),RCHFLX_out(iens, iRch_ups)%ROUTE(idxKW)%REACH_Q
+       write(iulog,'(A,1X,I12,1X,G15.4)') ' UREACHK, uprflux=',NETOPO_in(segIndex)%UREACHK(iUps),RCHFLX_out(iens, iRch_ups)%ROUTE(idxKW)%REACH_Q
      enddo
    end if
-   write(iulog,'(A,X,G15.4)') ' RCHFLX_out(iEns,segIndex)%BASIN_QR(1)=',RCHFLX_out(iEns,segIndex)%BASIN_QR(1)
+   write(iulog,'(A,1X,G15.4)') ' RCHFLX_out(iEns,segIndex)%BASIN_QR(1)=',RCHFLX_out(iEns,segIndex)%BASIN_QR(1)
  endif
 
  ! perform river network KW routing
@@ -208,11 +208,11 @@ SUBROUTINE kw_rch(iEns, segIndex, & ! input: index of runoff ensemble to be proc
                      doCheck,                            & ! input: reach index to be examined
                      ierr, cmessage)                       ! output: error control
  if(ierr/=0)then
-   write(message, '(A,X,I12,X,A)') trim(message)//'/segment=', NETOPO_in(segIndex)%REACHID, '/'//trim(cmessage); return
+   write(message, '(A,1X,I12,1X,A)') trim(message)//'/segment=', NETOPO_in(segIndex)%REACHID, '/'//trim(cmessage); return
  endif
 
  if(doCheck)then
-   write(iulog,'(A,X,G15.4)') ' RCHFLX_out(iens,segIndex)%REACH_Q=', RCHFLX_out(iens,segIndex)%ROUTE(idxKW)%REACH_Q
+   write(iulog,'(A,1X,G15.4)') ' RCHFLX_out(iens,segIndex)%REACH_Q=', RCHFLX_out(iens,segIndex)%ROUTE(idxKW)%REACH_Q
  endif
 
  END SUBROUTINE kw_rch
@@ -298,8 +298,8 @@ SUBROUTINE kinematic_wave(rch_param,     & ! input: river parameter data structu
    Q(1,0) = q_upstream
 
    if (doCheck) then
-     write(iulog,'(3(A,X,G12.5))') ' R_SLOPE=',rch_param%R_SLOPE,' R_WIDTH=',rch_param%R_WIDTH,' R_MANN=',rch_param%R_MAN_N
-     write(iulog,'(3(A,X,G12.5))') ' Q(0,0)=',Q(0,0),' Q(0,1)=',Q(0,1),' Q(1,0)=',Q(1,0)
+     write(iulog,'(3(A,1X,G12.5))') ' R_SLOPE=',rch_param%R_SLOPE,' R_WIDTH=',rch_param%R_WIDTH,' R_MANN=',rch_param%R_MAN_N
+     write(iulog,'(3(A,1X,G12.5))') ' Q(0,0)=',Q(0,0),' Q(0,1)=',Q(0,1),' Q(1,0)=',Q(1,0)
    end if
 
    ! ----------
@@ -340,7 +340,7 @@ SUBROUTINE kinematic_wave(rch_param,     & ! input: river parameter data structu
    endif
 
    if (doCheck) then
-     write(iulog,'(1(A,X,G15.4))') ' Q(1,1)=',Q(1,1)
+     write(iulog,'(1(A,1X,G15.4))') ' Q(1,1)=',Q(1,1)
    end if
 
  else ! if head-water
@@ -350,7 +350,7 @@ SUBROUTINE kinematic_wave(rch_param,     & ! input: river parameter data structu
 
    if (doCheck) then
      write(iulog,'(A)')            ' This is headwater '
-     write(iulog,'(1(A,X,G15.4))') ' Q(1,1)=',Q(1,1)
+     write(iulog,'(1(A,1X,G15.4))') ' Q(1,1)=',Q(1,1)
    endif
 
  endif