uneven timesteps for elev.th and flux.th

cmake/SCHISM.local.phil.bfg

@@ -0,0 +1,75 @@
+###W&M Whirlwind cluster
+#  Set the base name of the executable.
+#  The main reason for this is to include something like a cluster/architecture name.
+#  Do not add the file extension (none for linux, .exe for Windows etc)
+#  or the list of enabled modules, both of which will be automatically appended.
+set (SCHISM_EXE_BASENAME pschism_bfg CACHE STRING "Base name (modules and file extension to be added of the executable. If you want a machine name, add it here")
+
+
+
+##########################  LOCATIONS #########################################################
+#
+# LOCATIONS: Set locations for NetCDF (possibly HDF5 if NetCDF links to it), ParMetis, PETSc
+#            You don't need to set these if they are in your environment
+#
+#            Only the library home location is needed and the /lib or /bin part will be inferred.
+#            Generally traditional structure is assumed, but the Parmetis and GOTM libraries
+#            that are included have a slightly different structure
+#
+#            You only need GOTM if you intend to use it with USE_GOTM
+#            GOTM and ParMetis local copies will be found automatically, but also can overridden
+#            You have to build them
+#
+
+###Relative paths won't work
+set(CMAKE_Fortran_COMPILER mpif90 CACHE PATH "Path to serial Fortran compiler")
+set(NetCDF_FORTRAN_DIR "$ENV{NETCDF_FORTRAN}" CACHE PATH "Path to NetCDF Fortran library")
+set(NetCDF_C_DIR  "$ENV{NETCDF}"  CACHE PATH "Path to NetCDF C library")
+###MPI_ROOT is only needed when cmake is having trouble finding write MPI wrapper
+#set(MPI_ROOT /opt/mvapich2/2.3-intel CACHE PATH "Root dir of MPI implementation")
+
+#set(HDF5_DIR  /opt/hdf5/1.10.4-intel64 CACHE PATH "Path to HDF5")
+#set(SZIP_DIR /opt/szip/2.1.1-intel64 CACHE PATH "Path to SZip compression library")
+
+
+######################## COMPILE AND BUILD OPTIONS ##############################################
+#
+# BUILD OPTS: Use this to set compiler flags any way you want.For models of how to set flags, 
+#             see SCHISMCompile.cmake, which are the project defaults.
+#
+#             If you are setting up a new platform/compiler combo rather than customizing, 
+#             you might consider adding to SCHISMCompile.cmake with the correct "IF" so 
+#             others can profit from your work.
+#             
+#             If what you are doing is debugging, consider using -DBUILD_TYPE=Debug and using the default
+#             debug flags. Note that there is yet another build type for release plus symbols.
+#
+#             So far I have removed -Bstatic because it is causes problems and cmake seems to do enough
+#             magically.
+#
+#################################################################################################
+
+
+###Compile flags
+set(CMAKE_Fortran_FLAGS_RELEASE "-g " CACHE STRING "Fortran flags" FORCE)
+# set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -mcmodel=medium -assume byterecl" CACHE STRING "Fortran flags" FORCE)
+##For final linking: this is only needed in exordinary cases
+#set(CMAKE_EXE_LINKER_FLAGS "" CACHE STRING "linker" FORCE)
+
+###MPI_VERSION cannot be set here; use -DMPIVERSION=XX in cmake cmd instead
+#set(MPI_VERSION CACHE STRING  "1")
+
+###FABM usage
+set( USE_FABM ON   CACHE BOOLEAN "FABM BGC model interface")
+#If FABM is on, need to set FABM_BASE
+set(FABM_BASE /beegfs/home/Wyrwa/FABM/fabm4schism)
+
+################################################################################################# notes
+# [email protected]:~/SCHISM/github_schism17okt25/entwicklung> rsync -va . /beegfs/home/Wyrwa/SCHISM/github_schism17okt25
+# cmake -C ../cmake/SCHISM.local.build -C ../cmake/SCHISM.local.phil.bfg ../src/
+# cmake --build .
+#
+# previously:
+# [email protected]:~/SCHISM/github_schism17okt25/entwicklung> rsync -va ./src /beegfs/home/Wyrwa/SCHISM/github_schism17okt25/src
+# cmake -C ../cmake/SCHISM.local.build -C ../cmake/SCHISM.local.phil.bfg -DUSE_FABM=ON -DFABM_BASE=/beegfs/home/Wyrwa/FABM/fabm4schism -DFABM_EXTRA_INSTITUTES=uzweijens -DFABM_UZWEIJENS_BASE=../src/QSim/ ../src/
+# 

src/Hydro/schism_init.F90

@@ -445,13 +445,15 @@ subroutine schism_init(iorder,indir,iths,ntime)
       !just add the output statements in _step and flags in param.nml (same
       !order). Flags for modules other than hydro are only used inside USE_*
       if(iorder==0) then
-        allocate(iof_hydro(40),iof_wwm(40),iof_gen(max(1,ntracer_gen)),iof_age(max(1,ntracer_age)),level_age(ntracer_age/2), &
-     &iof_sed(3*sed_class+20),iof_eco(max(1,eco_class)),iof_icm_core(17),iof_icm_silica(2),iof_icm_zb(2),iof_icm_ph(4), &
-     &iof_icm_srm(4),iof_cos(20),iof_fib(5),iof_sed2d(14),iof_ice(10),iof_mice(10),iof_ana(20),iof_marsh(2),iof_dvd(max(1,ntrs(12))), &
-      !dim of srqst7 increased to account for 2D elem/side etc
-     &srqst7(nscribes+10),veg_vert_z(nbins_veg_vert+1),veg_vert_scale_cd(nbins_veg_vert+1), &
-     &veg_vert_scale_N(nbins_veg_vert+1),veg_vert_scale_D(nbins_veg_vert+1), &
-     &veg_di0(nmarsh_types),veg_h0(nmarsh_types),veg_nv0(nmarsh_types),veg_cd0(nmarsh_types),drown_marsh(nmarsh_types),stat=istat)
+        allocate(iof_hydro(40),iof_wwm(40),iof_gen(max(1,ntracer_gen)),iof_age(max(1,ntracer_age)),    &
+        &level_age(ntracer_age/2), iof_sed(3*sed_class+20),iof_eco(max(1,eco_class)),iof_icm_core(17), &
+        &iof_icm_silica(2),iof_icm_zb(2),iof_icm_ph(4), iof_icm_srm(4),iof_cos(20),iof_fib(5),         &
+        &iof_sed2d(14),iof_ice(10),iof_mice(10),iof_ana(20),iof_marsh(2),iof_dvd(max(1,ntrs(12))),     &
+        &srqst7(nscribes+10),veg_vert_z(nbins_veg_vert+1),veg_vert_scale_cd(nbins_veg_vert+1),         &
+        &veg_vert_scale_N(nbins_veg_vert+1),veg_vert_scale_D(nbins_veg_vert+1), veg_di0(nmarsh_types), &
+        &veg_h0(nmarsh_types),veg_nv0(nmarsh_types),veg_cd0(nmarsh_types),drown_marsh(nmarsh_types),   &
+        &stat=istat)
+        !dim of srqst7 increased to account for 2D elem/side etc
         if(istat/=0) call parallel_abort('INIT: iof failure')
         srqst7(:)=MPI_REQUEST_NULL
         !Global output on/off flags

src/Hydro/schism_step.F90

@@ -1407,59 +1407,55 @@ subroutine schism_step(it)
 !--------------------------------------------------------------------------
 !     Get new time series values from *.th
       if(nettype>0) then
-        if(time>th_time(1,2,1)) then !not '>=' to avoid last step
-          ath(:,1,1,1)=ath(:,1,2,1)
-          read(50,*) tmp,ath(1:nettype,1,2,1)
-          th_time(1,1,1)=th_time(1,2,1)
-          th_time(1,2,1)=th_time(1,2,1)+th_dt(1,1)
-        endif !time
-!        if(it==iths_main+1.and.abs(tmp-time)>1.e-4) then
-!          write(errmsg,*)'Starting time wrong for eta',it,tmp
-!          call parallel_abort(errmsg)
-!        endif
+         tmp=th_time(1,2,1)
+         do while(time>tmp)
+            ath(:,1,1,1)=ath(:,1,2,1)
+            read(50,*) tmp,ath(1:nettype,1,2,1)
+            th_time(1,1,1)=th_time(1,2,1)
+            th_time(1,2,1)=tmp
+            th_dt(1,1) = th_time(1,2,1)-th_time(1,1,1)
+         end do ! next timestep
 
-        rat=(time-th_time(1,1,1))/th_dt(1,1)
-        if(rat<-small1.or.rat>1.d0+small1) then
-          write(errmsg,*) 'STEP: rat out in elev.th:',rat,time,th_time(1,1:2,1),th_dt(1,1)
-          call parallel_abort(errmsg)
-        endif
-        icount=0
-        do k=1,nope_global
-          if(iettype(k)==1) then
-            icount=icount+1
-            if(icount>nettype) call parallel_abort('Wrong counting 1')
-            eth(1,k)=(1-rat)*ath(icount,1,1,1)+rat*ath(icount,1,2,1)
-          endif
-        enddo 
+         rat=(time-th_time(1,1,1))/th_dt(1,1)
+         if(rat<-small1.or.rat>1.d0+small1) then
+            write(errmsg,*) 'STEP: rat out in elev.th:',rat,time,th_time(1,1:2,1),th_dt(1,1)
+            call parallel_abort(errmsg)
+         endif
+         icount=0
+         do k=1,nope_global
+            if(iettype(k)==1) then
+               icount=icount+1
+               if(icount>nettype) call parallel_abort('Wrong counting 1')
+               eth(1,k)=(1-rat)*ath(icount,1,1,1)+rat*ath(icount,1,2,1)
+            endif
+         enddo 
       endif !nettype
 
       if(nfltype>0) then
-        if(time>th_time(1,2,2)) then
-          ath(:,1,1,2)=ath(:,1,2,2)
-          read(51,*) tmp,ath(1:nfltype,1,2,2)
-          th_time(1,1,2)=th_time(1,2,2)
-          th_time(1,2,2)=th_time(1,2,2)+th_dt(1,2)
-        endif !time
-!        if(it==iths_main+1.and.abs(tmp-time)>1.e-4) then
-!          write(errmsg,*)'Starting time wrong for flux',it,tmp,time
-!          call parallel_abort(errmsg)
-!        endif
-
-        rat=(time-th_time(1,1,2))/th_dt(1,2)
-        if(rat<-small1.or.rat>1.d0+small1) then
-          write(errmsg,*) 'STEP: ratio out of range while interpolating &
-     &flux.th. Probably times are not equally spaced or dt has changesd &
-     &from a prior run (ratio, time, th times):',rat,time,th_time(1,1:2,2)
-          call parallel_abort(errmsg)
-        endif
-        icount=0
-        do k=1,nope_global
-          if(ifltype(k)==1) then
-            icount=icount+1
-            if(icount>nfltype) call parallel_abort('STEP: wrong counting 2')
-            qthcon(k)=(1.d0-rat)*ath(icount,1,1,2)+rat*ath(icount,1,2,2)
-          endif
-        enddo !k
+         tmp=th_time(1,2,2)
+         do while(time>tmp)
+            ath(:,1,1,2)=ath(:,1,2,2)
+            read(51,*) tmp,ath(1:nfltype,1,2,2)
+            th_time(1,1,2)=th_time(1,2,2)
+            th_time(1,2,2)=tmp
+            th_dt(1,2) = th_time(1,2,2)-th_time(1,1,2)
+         end do ! next timestep
+
+         rat=(time-th_time(1,1,2))/th_dt(1,2)
+         if(rat<-small1.or.rat>1.d0+small1) then
+            write(errmsg,*) 'STEP: ratio out of range while interpolating &
+            &flux.th. Probably times are not equally spaced or dt has changesd &
+            &from a prior run (ratio, time, th times):',rat,time,th_time(1,1:2,2)
+            call parallel_abort(errmsg)
+         endif
+         icount=0
+         do k=1,nope_global
+            if(ifltype(k)==1) then
+               icount=icount+1
+               if(icount>nfltype) call parallel_abort('STEP: wrong counting 2')
+               qthcon(k)=(1.d0-rat)*ath(icount,1,1,2)+rat*ath(icount,1,2,2)
+            endif
+         enddo !k
       endif !nfltype
 
       do i=1,natrm
@@ -2145,7 +2141,8 @@ subroutine schism_step(it)
         irec2(2)=(it+1)*nstride_schout+irec0_schout-(istack(2)-1)*nrec_schout !->time step n+1 (new)
         if(istack(2)>istack(1)) then !if istack(2) not exisit (last record), use previous stack
           write(it_char,'(i72)')istack(2)
-          inquire(file=in_dir(1:len_in_dir)//'hydro_out/'//trim(adjustl(snames_schout(1)))//'_'//trim(adjustl(it_char))//'.nc',exist=ltmp)
+          inquire(file=  & 
+&in_dir(1:len_in_dir)//'hydro_out/'//trim(adjustl(snames_schout(1)))//'_'//trim(adjustl(it_char))//'.nc',exist=ltmp)
           if(.not.ltmp) then !not exist; use same stack and reset record #
             istack(2)=istack(1); irec2(2)=irec2(1)
           endif

src/Utility/Combining_Scripts/combine_output11.f90

@@ -12,7 +12,8 @@
 ! Output: combined nc file
 !
 
-!  ifort -cpp -O2 -assume byterecl -o combine_output11.exe ../UtilLib/argparse.f90 ../UtilLib/schism_geometry.f90 combine_output11.f90 -I$NETCDF/include -I$NETCDF_FORTRAN/include -L$NETCDF_FORTRAN/lib -L$NETCDF/lib -lnetcdf -lnetcdff
+!  ifort -cpp -O2 -assume byterecl -o combine_output11.exe ../UtilLib/argparse.f90 ../UtilLib/schism_geometry.f90 & 
+!  & combine_output11.f90 -I$NETCDF/include -I$NETCDF_FORTRAN/include -L$NETCDF_FORTRAN/lib -L$NETCDF/lib -lnetcdf -lnetcdff
 
 !  History: 
 !          2018-1      Richard Hofmeister changed the combine method (all vars read in at a
@@ -989,7 +990,8 @@ subroutine combine_output11_input(ibgn,iend,iwetdry,to_be_combined,output_prefix
 !files=""
 
 cmd_name = "combine_output11"
-call cla_init(cmd_name,"Combine time blocked per-processor binary outputs (e.g. 'schout_000000_1.nc') into time blocked global outputs ('schout_1.nc')")
+call cla_init(cmd_name,"Combine time blocked per-processor binary outputs (e.g. 'schout_000000_1.nc') &
+&into time blocked global outputs ('schout_1.nc')")
 
 !call cla_register('-i','--in', 'input file (e.g. combine_input.in) containing options (overridden by command line specs)', cla_char,'')
 call cla_register('-b','--begin', 'start day', cla_int,'-1')

src/Utility/Post-Processing-Fortran/read_output10_xyz.f90

@@ -63,7 +63,8 @@ program read_out
       read(*,*)ibp
       if(ibp/=1.and.ibp/=2) stop 'Unknown format'
 
-      print*, 'Input ics (1-linear interp; 2-nearest neighbor interp. 2 for node-based variables only! 2 is suggested for sub-meter resolution!):'
+      print*, 'Input ics (1-linear interp; 2-nearest neighbor interp. 2 for node-based variables only! &
+      &       2 is suggested for sub-meter resolution!):'
       read(*,*)ics
 
       print*, 'Input variable name to read from nc (e.g. elevation):'

src/Utility/Post-Processing-Fortran/read_output9_xyz.f90

@@ -79,7 +79,8 @@ program read_out
       read(*,*)ibp
       if(ibp/=1.and.ibp/=2) stop 'Unknown format'
 
-      print*, 'Input ics (1-linear interp; 2-nearest neighbor interp. 2 for node-based variables only! 2 is suggested for sub-meter resolution!):'
+      print*, 'Input ics (1-linear interp; 2-nearest neighbor interp. 2 for node-based variables only!  &
+      &       2 is suggested for sub-meter resolution!):'
       read(*,*)ics
 
       print*, 'Input variable name to read from nc (e.g. elev):'