Merge pull request #575 from feathern/writesix

Removal of Write(6,*)

src/Diagnostics/Diagnostics_Base.F90

@@ -146,13 +146,6 @@ Module Diagnostics_Base
     Integer :: lforce_r, lforcepp_r, lforcemm_r
 Contains
 
-    Subroutine Generate_Diagnostic_Labels()
-        ! Define labels for our quantity codes
-        Write(6,*)'A line of code.'
-        !Call Load_Label(v_r,'V_r')
-        !Call Load_Label(v_theta,'V_theta')
-        !Call Load_Label(v_phi, 'V_phi')
-    End Subroutine Generate_Diagnostic_Labels
 
     Subroutine Initialize_Diagnostics_Buffer()
         Logical :: dbtrans, dbconfig

src/Diagnostics/Diagnostics_Custom.F90

@@ -210,23 +210,20 @@ Subroutine Custom_Hydro_Diagnostics(buffer)
         !END_DO
 
         If (compute_quantity(ell0_vr)) Then
-            Write(6,*)'Ell0_vr', ell0_vr
             DO_PSI
                 qty(PSI) = ell0_values(r,vr)
             END_DO
             Call Add_Quantity(qty)
         Endif
 
         If (compute_quantity(ell0_tvar)) Then
-            Write(6,*)'Ell0 tvar', ell0_tvar
             DO_PSI
                 qty(PSI) = ell0_values(r,tvar)
             END_DO
             Call Add_Quantity(qty)
         Endif
 
         If (compute_quantity(ell0_dpdr)) Then
-            Write(6,*)'Ell0 tvar', ell0_dpdr
             DO_PSI
                 qty(PSI) = ell0_values(r,dpdr)
             END_DO

src/Diagnostics/Diagnostics_Interface.F90

@@ -376,7 +376,6 @@ Subroutine Reboot_Diagnostics(iteration,force_reboot)
             Endif
         Else
             If (MOD(iteration,diagnostic_reboot_interval) .eq. 0) Then
-                if (my_rank .eq. 0) WRITE(6,*)'REBOOTING DIAGNOSTICS!'
                 ! Find the name of the current reboot file.
                 ndigits = count_digits(reboot_count)
                 Write(ndigstr,'(i1.1)') ndigits

src/Diagnostics/Diagnostics_Mean_Correction.F90

@@ -437,7 +437,6 @@ Subroutine Mean_Correction(buffer)
         !//////////////////////////////////////////////////////
         ! Perform the averaging
         if (compute_mean_correct) then
-            !Write(6,*)'Allocated: ', allocated(mean_3dbuffer), allocated(mean_ell0buffer)
 
             Call ComputeEll0(mean_3dbuffer,mean_ell0buffer)
         endif

src/Diagnostics/Diagnostics_Miscellaneous.F90

@@ -40,7 +40,6 @@ Subroutine Compute_Misc_Diagnostics(buffer)
                 qty(PSI) = sin(k*2.0d0*mypi/n_phi) &
                     & *(sintheta(t)**2)*radius(r)
             END_DO
-            Write(6,*)'Diagnostic1!', my_rank
             Call Add_Quantity(qty)
         Endif
 

src/Diagnostics/Diagnostics_Second_Derivatives.F90

@@ -309,7 +309,7 @@ Subroutine Initialize_Second_Derivatives()
         Call d2buffer%init(field_count = ddfcount, config = 'p3b')
 
         Call d2buffer%construct('p3a')
-        !WRITE(6,*)'BCHECK: ', shape(d2buffer%p3a)
+
         Call d2buffer%deconstruct('p3a')
     End Subroutine Initialize_Second_Derivatives
 
@@ -350,20 +350,17 @@ Subroutine Compute_Second_Derivatives(inbuffer)
 
         !///////////////////////////////////////////////////////////
         ! Step 1: Initialize p3b portion of d2buffer
-        !Write(6,*)'Constructing the buffer...', d2buffer%nf3b
 
         Call d2buffer%construct('p3b')
         d2buffer%config = 'p3b'
 
-        !Write(6,*)'Complete...'
 
         !///////////////////////////////////////////////////////////
         ! Steps 2-3:  Load radial and theta derivatives
         Do i = 1, nddfields*2
             d2buffer%p3b(:,:,:,ddindmap(1,i)) = inbuffer(:,:,:,ddindmap(2,i))
         Enddo
 
-        !Write(6,*)'Steps 1-3 complete.'
 
         !////////////////////////////////////////////////////////////////
         ! Step 4:  Move to p1b/p1a configuration
@@ -388,7 +385,6 @@ Subroutine Compute_Second_Derivatives(inbuffer)
         d2buffer%p1b = 0.0
         d2buffer%config='p1a'
 
-        !Write(6,*)'Steps 4 complete.'
 
         !////////////////////////////////////////////////////////////
         ! Steps 5-6:  Load d2_by_dr2 and d2_by_drdt into the buffer
@@ -408,17 +404,14 @@ Subroutine Compute_Second_Derivatives(inbuffer)
         Call d2buffer%deconstruct('p1b')
 
         ! Ordering of fields in buffer is now dxdr, dxdt, dxdrdr, dxdrdt
-        !Write(6,*)'Steps 5-6 complete.'
 
         !///////////////////////////////////////////////////////////////
         ! Step 7:  Move to s2a & overwrite dxdt with sintheta*{dxdtdt}
         Call d2buffer%reform()
 
-        !Write(6,*)'Step 7 reformation complete'
 
         Call Allocate_rlm_Field(ddtemp)
 
-        !Write(6,*)'Step 7 allocation complete', nddfields
 
         Do i = nddfields+1,nddfields*2
             ! We overwrite dxdt with sintheta* {dxdtdt}
@@ -428,18 +421,15 @@ Subroutine Compute_Second_Derivatives(inbuffer)
             END_DO
         Enddo
 
-        !Write(6,*)'Step 7 derivatves complete'
 
         Call DeAllocate_rlm_Field(ddtemp)
 
-        !Write(6,*)'Step 7 deallocation complete'
 
         Call d2buffer%construct('p2a')
         Call Legendre_Transform(d2buffer%s2a,d2buffer%p2a)
         Call d2buffer%deconstruct('s2a')
         d2buffer%config = 'p2a'
 
-        !Write(6,*)'Step 7 complete.'
 
         !/////////////////////////////////////////////////////////////////////
         !  Steps 8-10 : phi derivatives
@@ -478,7 +468,6 @@ Subroutine Compute_Second_Derivatives(inbuffer)
         Enddo
 
         Call d2buffer%deconstruct('p3b')
-       ! Write(6,*)'Steps 8-10 complete.'
 
         !//////////////////////////////////////////
         ! Step 11:   Finalize
@@ -510,7 +499,6 @@ Subroutine Compute_Second_Derivatives(inbuffer)
             END_DO
         ENDDO
 
-        !Write(6,*)'Step 11 complete.'
     End Subroutine Compute_Second_Derivatives
 
     Subroutine Allocate_rlm_Field(arr)

src/Diagnostics/Diagnostics_TurbKE_Budget.F90

@@ -199,7 +199,6 @@ Subroutine Compute_TurbulentKE_Budget(buffer)
         ! Viscous Transport of turbulent kinetic energy.
         !    -div.F_TV = div.(sigma'.u') = (div.sigma').u' + Phi_T
         If (compute_quantity(transport_viscous_pKE)) Then
-            !Write(6,*)dvrdrdr, shape(d2_fbuffer)
             DO_PSI2
                 one_over_rsin = one_over_r(r) * csctheta(t)
                 ctn_over_r = one_over_r(r) * cottheta(t)

src/IO/Spherical_IO.F90

@@ -849,6 +849,7 @@ Subroutine Initialize_Diagnostic_Info(self,computes,mpi_tag, &
         Integer :: avg_axes(1:3), ecode
         Integer, Allocatable :: indices(:,:)
         Real*8, Allocatable :: avg_weights(:,:)
+        Character*8 :: cache_str, rec_str
         Class(DiagnosticInfo) :: self 
 
         nonstandard=.false.
@@ -892,19 +893,21 @@ Subroutine Initialize_Diagnostic_Info(self,computes,mpi_tag, &
 
 
         !Check that the cache size is appropriate
+        Write(cache_str,'(i8)')self%cache_size
+        Write(rec_str,'(i8)')self%rec_per_file       
         If (present(cache_size)) Then
             If (cache_size .ge. 1) Then
                 self%cache_size = cache_size
             Endif
         Endif
         If (self%cache_size .lt. 1) Then
             If (myid .eq. 0) Then
-                    Write(6,*)'////////////////////////////////////////////////////////////////////'
-                    Write(6,*)'   Warning:  Incorrect cache_size specification for ',self%file_prefix
-                    Write(6,*)'   Cache_size must be at least 1.'
-                    Write(6,*)'   Specified cache_size: ', self%cache_size
-                    Write(6,*)'   Caching has been deactivated for ', self%file_prefix
-                    Write(6,*)'////////////////////////////////////////////////////////////////////'                    
+                    Call stdout%print('////////////////////////////////////////////////////////////////////')
+                    Call stdout%print('   Warning:  Incorrect cache_size specification for '//TRIM(ADJUSTL(self%file_prefix)))
+                    Call stdout%print('   Cache_size must be at least 1.')
+                    Call stdout%print('   Specified cache_size: '//TRIM(ADJUSTL(cache_str)) )
+                    Call stdout%print('   Caching has been deactivated for '//TRIM(ADJUSTL(self%file_prefix)) )
+                    Call stdout%print('////////////////////////////////////////////////////////////////////')                    
             Endif
             self%cache_size = 1
         Endif
@@ -913,13 +916,13 @@ Subroutine Initialize_Diagnostic_Info(self,computes,mpi_tag, &
             If (modcheck .ne. 0) Then
 
                 If (myid .eq. 0) Then
-                    Write(6,*)'////////////////////////////////////////////////////////////////////'
-                    Write(6,*)'   Warning:  Incorrect cache_size specification for ',self%file_prefix
-                    Write(6,*)'   Cache_size cannot be larger than nrec.'
-                    Write(6,*)'   Cache_size: ', self%cache_size
-                    Write(6,*)'   nrec      : ', self%rec_per_file
-                    Write(6,*)'   Cache_size has been set to nrec.'
-                    Write(6,*)'////////////////////////////////////////////////////////////////////'                    
+                    Call stdout%print('////////////////////////////////////////////////////////////////////')
+                    Call stdout%print('   Warning:  Incorrect cache_size specification for '//TRIM(ADJUSTL(self%file_prefix)) )
+                    Call stdout%print('   Cache_size cannot be larger than nrec.')
+                    Call stdout%print('   Cache_size: '//TRIM(ADJUSTL(cache_str)))
+                    Call stdout%print('   nrec      : '//TRIM(ADJUSTL(rec_str)))
+                    Call stdout%print('   Cache_size has been set to nrec.')
+                    Call stdout%print('////////////////////////////////////////////////////////////////////')                    
                 Endif
                 self%cache_size = self%rec_per_file
             Endif
@@ -930,13 +933,13 @@ Subroutine Initialize_Diagnostic_Info(self,computes,mpi_tag, &
             If (modcheck .ne. 0) Then
 
                 If (myid .eq. 0) Then
-                    Write(6,*)'////////////////////////////////////////////////////////////////////'
-                    Write(6,*)'   Warning:  Incorrect cache_size specification for ',self%file_prefix
-                    Write(6,*)'   Cache_size must divide evenly into nrec.'
-                    Write(6,*)'   Cache_size: ', self%cache_size
-                    Write(6,*)'   nrec      : ', self%rec_per_file
-                    Write(6,*)'   Caching has been deactivated for ', self%file_prefix
-                    Write(6,*)'////////////////////////////////////////////////////////////////////'                    
+                    Call stdout%print('////////////////////////////////////////////////////////////////////')
+                    Call stdout%print('   Warning:  Incorrect cache_size specification for '//TRIM(ADJUSTL(self%file_prefix)) )
+                    Call stdout%print('   Cache_size must divide evenly into nrec.')
+                    Call stdout%print('   Cache_size: '//TRIM(ADJUSTL(cache_str)))
+                    Call stdout%print('   nrec      : '//TRIM(ADJUSTL(rec_str)))
+                    Call stdout%print('   Caching has been deactivated for '//TRIM(ADJUSTL(self%file_prefix)) )
+                    Call stdout%print('////////////////////////////////////////////////////////////////////')                    
                 Endif
                 self%cache_size = 1
             Endif
@@ -1295,13 +1298,18 @@ Subroutine CloseFile_Par(self)
         Implicit None
         integer :: ierr, buffsize
         integer(kind=MPI_OFFSET_KIND) :: disp
+        Character*8 :: err_str, id_str
         !Parallel File Close
         !Peforms the same task as closefile, but using MPI-IO
         Class(DiagnosticInfo) :: self
         disp = 8
         Call MPI_File_Seek(self%file_unit,disp,MPI_SEEK_SET,ierr)
+
         If (ierr .ne. 0) Then
-            Write(6,*)'Error rewinding to header.  Error code: ', ierr, myid, self%file_prefix
+            Write(err_str,'(i8)')ierr
+            Write(id_str,'(i8)')myid
+            Call stdout%print('Error rewinding to header.  Error code: '//TRIM(err_str)//','//TRIM(id_str)//self%file_prefix)
+
         Endif
         ! Without this barrier,  the record update below can occurs before some ranks
         ! have read the original record count (leading to oversized, corrupted files).
@@ -1312,10 +1320,14 @@ Subroutine CloseFile_Par(self)
 
             call MPI_FILE_WRITE(self%file_unit,self%current_rec , buffsize, MPI_INTEGER, & 
                 MPI_STATUS_IGNORE, ierr) 
-            If (ierr .ne. 0) Write(6,*)'Error writing to header.  Error code: ', ierr, myid, self%file_prefix
+            If (ierr .ne. 0) Then
+                Call stdout%print('Error writing to header.  Error code: '//TRIM(err_str)//','//TRIM(id_str)//self%file_prefix)           
+            Endif
         Endif
         Call MPI_FILE_CLOSE(self%file_unit, ierr)
-        If (ierr .ne. 0) Write(6,*)'Error closing file.  Error code: ',ierr, myid, self%file_prefix
+        If (ierr .ne. 0) Then
+            Call stdout%print('Error closing file.  Error code: '//TRIM(err_str)//','//TRIM(id_str)//self%file_prefix)         
+        Endif 
     End Subroutine CloseFile_Par
 
     Subroutine getq_now(self,yesno)

src/Makefile.fdeps

@@ -1,5 +1,5 @@
 All_to_All.o : All_to_All.F90 Ra_MPI_Base.o 
-Benchmarking.o : Benchmarking.F90 Initial_Conditions.o BoundaryConditions.o Math_Constants.o PDE_Coefficients.o Legendre_Polynomials.o Fields.o Spherical_IO.o Controls.o ProblemSize.o 
+Benchmarking.o : Benchmarking.F90 BufferedOutput.o Initial_Conditions.o BoundaryConditions.o Math_Constants.o PDE_Coefficients.o Legendre_Polynomials.o Fields.o Spherical_IO.o Controls.o ProblemSize.o 
 BoundaryConditions.o : BoundaryConditions.F90 Controls.o Checkpointing.o PDE_Coefficients.o Generic_Input.o Load_Balance.o Fields.o ProblemSize.o Math_Constants.o 
 BufferedOutput.o : BufferedOutput.F90 
 Chebyshev_Polynomials.o : Chebyshev_Polynomials.F90 Structures.o 
@@ -39,7 +39,7 @@ Fourier_Derivatives.o : Fourier_Derivatives.F90
 Fourier_Transform.o : Fourier_Transform.F90 Parallel_Framework.o 
 General_IO.o : General_IO.F90 General_MPI.o Parallel_Framework.o 
 General_MPI.o : General_MPI.F90 Ra_MPI_Base.o 
-Generic_Input.o : Generic_Input.F90 ProblemSize.o SendReceive.o Load_Balance.o Spherical_Buffer.o Parallel_Framework.o Ra_MPI_Base.o 
+Generic_Input.o : Generic_Input.F90 BufferedOutput.o ProblemSize.o SendReceive.o Load_Balance.o Spherical_Buffer.o Parallel_Framework.o Ra_MPI_Base.o 
 ISendReceive.o : ISendReceive.F90 Ra_MPI_Base.o 
 Initial_Conditions.o : Initial_Conditions.F90 Load_Balance.o BufferedOutput.o Math_Utility.o Linear_Solve.o ClockInfo.o BoundaryConditions.o PDE_Coefficients.o General_MPI.o Timers.o Controls.o Generic_Input.o Checkpointing.o Math_Constants.o SendReceive.o Legendre_Transforms.o Fourier_Transform.o Parallel_Framework.o Fields.o ProblemSize.o 
 Input.o : Input.F90 MPI_LAYER.o Ra_MPI_Base.o Checkpointing.o Parallel_Framework.o PDE_Coefficients.o TestSuite.o Initial_Conditions.o BoundaryConditions.o Spherical_IO.o Controls.o ProblemSize.o 
@@ -68,7 +68,7 @@ Sphere_Hybrid_Space.o : Sphere_Hybrid_Space.F90 indices.F PDE_Coefficients.o Clo
 Sphere_Linear_Terms.o : Sphere_Linear_Terms.F90 Math_Constants.o PDE_Coefficients.o ClockInfo.o Timers.o BoundaryConditions.o Fields.o Linear_Solve.o ProblemSize.o Controls.o Load_Balance.o 
 Sphere_Physical_Space.o : Sphere_Physical_Space.F90 indices.F Benchmarking.o Math_Constants.o PDE_Coefficients.o ClockInfo.o Timers.o General_MPI.o Diagnostics_Interface.o Fields.o Spectral_Derivatives.o Fourier_Transform.o ProblemSize.o Controls.o Parallel_Framework.o 
 Sphere_Spectral_Space.o : Sphere_Spectral_Space.F90 Sphere_Linear_Terms.o Timers.o ClockInfo.o BoundaryConditions.o Fields.o Linear_Solve.o Finite_Difference.o ProblemSize.o Controls.o Parallel_Framework.o Load_Balance.o 
-Spherical_Buffer.o : Spherical_Buffer.F90 Timers.o General_MPI.o Load_Balance.o Structures.o Parallel_Framework.o MPI_LAYER.o 
+Spherical_Buffer.o : Spherical_Buffer.F90 BufferedOutput.o Timers.o General_MPI.o Load_Balance.o Structures.o Parallel_Framework.o MPI_LAYER.o 
 Spherical_IO.o : Spherical_IO.F90 Ra_MPI_Base.o Parallel_IO.o MakeDir.o Math_Constants.o BufferedOutput.o Legendre_Transforms.o Fourier_Transform.o General_MPI.o ISendReceive.o SendReceive.o Parallel_Framework.o Spherical_Buffer.o 
 Structures.o : Structures.F90 
 TestSuite.o : TestSuite.F90 ProblemSize.o Test_Cheby.o Test_SHT.o 

src/Math_Layer/Chebyshev_Polynomials.F90

@@ -357,9 +357,7 @@ Subroutine dealias_buffer4d(self, buffer)
         Integer :: bsize(4), i,j,k,n,offset, ind1,ind2
 
         bsize = shape(buffer)
-        !do n = 1, self%domain_count
-        !    WRite(6,*)'da check: ', self%rda(n), self%npoly(n)
-        !Enddo
+
         Do k = 1, bsize(4)
         Do j = 1, bsize(3)
         Do i = 1, bsize(2)

src/Math_Layer/Finite_Difference.F90

@@ -233,7 +233,7 @@ Subroutine d_by_dx3d(field, dfield)
             stencil_radius = stencil_size/2
             stencil_center = stencil_radius+1
             offset = (N_S-stencil_size)/2
-            Write(6,*)'I am in and dorder is : ', d
+
             Do jj = jjmin, jjmax
                 Do ii = iimin, iimax
 
@@ -543,7 +543,7 @@ Subroutine Generate_Coefs(grid,n_stencil,coefs,deriv_order, boundary_accuracy)
         !
         !    Currently only type 1 is supported by the derivative routines and Implicit.F
         !*****************************************************************************************************
-        !Write(6,*)deriv_order
+
          ngrid = Size(grid)
         stencil_radius = n_stencil/2
         stencil_center = stencil_radius+1
@@ -594,7 +594,6 @@ Subroutine Generate_Coefs(grid,n_stencil,coefs,deriv_order, boundary_accuracy)
             dsum = zero
 
             Do j = jstart, jend
-                !Write(6,*)i,jstart,jend,stencil_center
                 dees(j) = grid(i+j-stencil_center)-grid(i)
                 dsum = dsum+ABS(dees(j))
             Enddo

src/Math_Layer/Fourier_Transform.F90

@@ -47,9 +47,7 @@ Subroutine Initialize_FFTs()
                 !Note that when using MKL, iret will be 0 always.
                 !iret = 0 means an error when using normal FFTW, but for MKL
                 ! This routine is a wrapper that does nothing.
-            !write(6,*)"iret is: ", iret
-            ! comment
-            !write(6,*)"FFTW planning with nthreads: ", nthread
+
             call dfftw_plan_with_nthreads(nthread)
         Endif
 #endif

src/Math_Layer/Legendre_Polynomials.F90

@@ -77,7 +77,6 @@ Subroutine DeAllocate_Plms(depar)
     Endif
     If (present(depar)) Then
         If (depar .and. parity) Then
-            Write(6,*)'DeAllocating Parity Arrays'
             Call DeAllocate_Parity_Plms()
         Endif
     Endif

src/Math_Layer/Legendre_Transforms.F90

@@ -1011,7 +1011,7 @@ Subroutine StP_4d_dgp2(data_in, data_out)
         If (n_l_even(m) .gt. 0) then
 
             jend = n_l_even(m)
-            !write(6,*)jend,rmn,rmx,nfield
+
             Allocate(temp3(1:jend,rmn:rmx,1:2,1:nfield))
             Do f = 1, nfield
             Do imi = 1, 2