faster io on juwels through chunking

FESOM · Jun 30, 2020 · 9bce28a · 9bce28a
1 parent d4139d9
commit 9bce28a
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Showing 4 changed files with 33 additions and 15 deletions.
diff --git a/env.sh b/env.sh
@@ -41,7 +41,7 @@ elif [[  $LOGINHOST = ubuntu ]]; then
    STRATEGY="ubuntu"
 elif [[  $LOGINHOST = bsc ]]; then
    STRATEGY="bsc"
-elif [[  $LOGINHOST =~ ^juwels[0-9]+\.fz\-juelich\.de$ ]]; then
+elif [[  $LOGINHOST =~ ^juwels[0-9]+\.ib\.juwels\.fzj\.de$ ]]; then
    STRATEGY="juwels"
 else
    echo "can not determine environment for host: "$LOGINHOST

diff --git a/src/ice_thermo_cpl.F90 b/src/ice_thermo_cpl.F90
@@ -118,17 +118,17 @@ subroutine thermodynamics(mesh)
      rsf     = 0._WP
 #endif
 
-#if defined (__oifs)
-     !---- different lead closing parameter for NH and SH
-     call r2g(geolon, geolat, coord_nod2d(1,inod), coord_nod2d(2,inod))
-     if (geolat.lt.0.) then
-        h0min = 0.75
-        h0max = 1.0
-     else
-        h0min = 0.5
-        h0max = 0.75
-     endif
-#endif /* (__oifs) */
+!#if defined (__oifs)
+!     !---- different lead closing parameter for NH and SH
+!     call r2g(geolon, geolat, coord_nod2d(1,inod), coord_nod2d(2,inod))
+!     if (geolat.lt.0.) then
+!        h0min = 0.75
+!        h0max = 1.0
+!     else
+!        h0min = 0.5
+!        h0max = 0.75
+!     endif
+!#endif /* (__oifs) */
 
      call ice_growth
 #if defined (__oifs)

diff --git a/src/io_meandata.F90 b/src/io_meandata.F90
@@ -591,6 +591,13 @@ subroutine create_new_file(entry)
      entry%error_status(c) = nf_put_att_real(entry%ncid, entry%varID, 'scale_factor', NF_REAL, 1, entry%scale_factor); c=c+1
      entry%error_status(c) = nf_put_att_real(entry%ncid, entry%varID, 'add_offset',   NF_REAL, 1, entry%add_offset);   c=c+1
   endif
+
+  if (entry%ndim==1) then
+     entry%error_status(c) = nf_def_var_chunking(entry%ncid, entry%varID, NF_CHUNKED, (/1/)); c=c+1
+  elseif (entry%ndim==2) then
+     entry%error_status(c) = nf_def_var_chunking(entry%ncid, entry%varID, NF_CHUNKED, (/1,  entry%glsize(1)/)); c=c+1
+  endif
+
   entry%error_status(c)=nf_put_att_text(entry%ncid, entry%varID, 'description', len_trim(entry%description), entry%description); c=c+1
   entry%error_status(c)=nf_put_att_text(entry%ncid, entry%varID, 'units',       len_trim(entry%units),       entry%units);       c=c+1
   entry%error_status(c)=nf_close(entry%ncid); c=c+1

diff --git a/src/io_restart.F90 b/src/io_restart.F90
@@ -307,10 +307,14 @@ subroutine create_new_file(id)
         do l=1, id%ndim ! list all defined dimensions 
            if (kdim==id%dim(l)%size) dimid(k)=id%dim(l)%code
         end do
-!________write(*,*) kdim, ' -> ', dimid(k)__________________________________
+        !write(*,*) "j",j,kdim, ' -> ', dimid(k)
      end do
-     id%error_status(c) = nf_def_var(id%ncid, trim(id%var(j)%name), NF_DOUBLE, id%var(j)%ndim+1, &
-                       (/dimid(1:n), id%rec/), id%var(j)%code); c=c+1
+     id%error_status(c) = nf_def_var(id%ncid, trim(id%var(j)%name), NF_DOUBLE, id%var(j)%ndim+1, (/dimid(1:n), id%rec/), id%var(j)%code); c=c+1
+     if (n==1) then
+        id%error_status(c)=nf_def_var_chunking(id%ncid, id%var(j)%code, NF_CHUNKED, (/1/)); c=c+1 
+     elseif (n==2) then
+        id%error_status(c)=nf_def_var_chunking(id%ncid, id%var(j)%code, NF_CHUNKED, (/1, id%dim(1)%size/)); c=c+1 
+     end if
      id%error_status(c)=nf_put_att_text(id%ncid, id%var(j)%code, 'description', len_trim(id%var(j)%longname), id%var(j)%longname); c=c+1
      id%error_status(c)=nf_put_att_text(id%ncid, id%var(j)%code, 'units',       len_trim(id%var(j)%units),    id%var(j)%units);    c=c+1
   end do
@@ -430,6 +434,7 @@ subroutine write_restart(id, istep, mesh)
   real(kind=WP), allocatable    :: aux(:), laux(:)
   integer                       :: i, lev, size1, size2, shape
   integer                       :: c
+  real(kind=WP)                 :: t0, t1, t2, t3
 
 #include  "associate_mesh.h"
 
@@ -451,6 +456,7 @@ subroutine write_restart(id, istep, mesh)
      if (shape==1) then
         size1=id%var(i)%dims(1)
         if (mype==0) allocate(aux(size1))
+        t0=MPI_Wtime()
         if (size1==nod2D)  call gather_nod (id%var(i)%pt1, aux)
         if (size1==elem2D) call gather_elem(id%var(i)%pt1, aux)
         if (mype==0) then
@@ -468,11 +474,16 @@ subroutine write_restart(id, istep, mesh)
            laux=id%var(i)%pt2(lev,:)
 !          if (size1==nod2D  .or. size2==nod2D)  call gather_nod (id%var(i)%pt2(lev,:), aux)
 !          if (size1==elem2D .or. size2==elem2D) call gather_elem(id%var(i)%pt2(lev,:), aux)
+           t0=MPI_Wtime()
            if (size1==nod2D  .or. size2==nod2D)  call gather_nod (laux, aux)
            if (size1==elem2D .or. size2==elem2D) call gather_elem(laux, aux)
+           t1=MPI_Wtime()
            if (mype==0) then
               id%error_status(c)=nf_put_vara_double(id%ncid, id%var(i)%code, (/lev, 1, id%rec_count/), (/1, size2, 1/), aux, 1); c=c+1
            end if
+           t2=MPI_Wtime()
+           if (mype==0 .and. size2==nod2D) write(*,*) 'nvar: ', i, 'lev: ', lev, 'gather_nod: ', t1-t0
+           if (mype==0 .and. size2==nod2D) write(*,*) 'nvar: ', i, 'lev: ', lev, 'nf_put_var: ', t2-t1
         end do
         deallocate(laux)
         if (mype==0) deallocate(aux)