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Add fixes to OznMon. #36

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Jul 15, 2020
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Add fixes to OznMon. #36

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39 changes: 29 additions & 10 deletions util/Ozone_Monitor/CMakeLists.txt
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
cmake_minimum_required(VERSION 2.6)
cmake_minimum_required(VERSION 2.8)
if(CMAKE_SOURCE_DIR STREQUAL CMAKE_CURRENT_SOURCE_DIR)
# I am top-level project.
if( NOT DEFINED ENV{CC} )
find_path( crayComp "ftn" )
# find_path( wcossIntel "mpfort" )
find_path( wcossIntel "mpfort" )
find_path( intelComp "ifort" )
find_path( pgiComp "pgf90" )
if( crayComp )
Expand All @@ -22,7 +22,7 @@ if(CMAKE_SOURCE_DIR STREQUAL CMAKE_CURRENT_SOURCE_DIR)
message("Setting env for wcoss intel")
set(ENV{CC} "mpcc")
set(ENV{CXX} "mpCC")
# set(ENV{FC} "mpfort")
set(ENV{FC} "mpfort")
endif()
if( pgiComp )
set(ENV{CC} "pgcc")
Expand All @@ -32,8 +32,8 @@ if(CMAKE_SOURCE_DIR STREQUAL CMAKE_CURRENT_SOURCE_DIR)
endif()
project(COV_Calc)
enable_language (Fortran)
# find_package(OpenMP)
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/../../cmake/Modules/")
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/lib")
include(${CMAKE_SOURCE_DIR}/../../cmake/Modules/setPlatformVariables.cmake)
include(${CMAKE_SOURCE_DIR}/../../cmake/Modules/setIntelFlags.cmake)
include(${CMAKE_SOURCE_DIR}/../../cmake/Modules/setGNUFlags.cmake)
Expand Down Expand Up @@ -64,20 +64,40 @@ if(CMAKE_SOURCE_DIR STREQUAL CMAKE_CURRENT_SOURCE_DIR)
message("Setting PGI flags")
setPGI()
endif()

cmake_policy(SET CMP0009 NEW)
find_package(OpenMP)
message("found openmp with flag ${OPENMP_Fortran_FLAGS}")

# Set Host specific flags and options
setHOST()

if(FIND_HDF5_HL)
find_package(HDF5 COMPONENTS C HL Fortran_HL )
elseif(FIND_HDF5)
find_package(HDF5)
endif()

find_package(MPI REQUIRED)
message("MPI version is ${MPI_Fortran_VERSION}")
message("MPI f90 version is ${MPI_Fortran_HAVE_F90_MODULE}")
message("MPI f08 version is ${MPI_Fortran_HAVE_F08_MODULE}")

add_definitions(${MPI_Fortran_COMPILE_FLAGS})
include_directories(${MPI_Fortran_INCLUDE_DIRS} ${MPI_INCLUDE_PATH} "./" ${CMAKE_INCLUDE_OUTPUT_DIRECTORY})
link_directories(${MPI_Fortran_LIBRARIES} ${ARCHIVE_OUTPUT_PATH} )
find_package( NetCDF REQUIRED)
if(FIND_HDF5_HL)
find_package(HDF5 COMPONENTS C HL Fortran_HL )
elseif(FIND_HDF5)
find_package(HDF5)
if(NETCDF4)
if(CMAKE_MAJOR_VERSION GREATER 2)
find_package( ZLIB )
endif()
find_package( CURL )
endif()

find_package( W3NCO )
set(NCDIAG_INCS "${PROJECT_BINARY_DIR}/libsrc/ncdiag")

set(BUILD_NCDIAG ON)
set(NCDIAG_INCS "${PROJECT_BINARY_DIR}/libsrc/ncdiag")
add_subdirectory(${PROJECT_SOURCE_DIR}/../../src/ncdiag ${PROJECT_BINARY_DIR}/libsrc/ncdiag)
set(NCDIAG_LIBRARIES ncdiag )
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
Expand All @@ -86,4 +106,3 @@ endif()
add_subdirectory(nwprod/oznmon_shared.v2.0.0/sorc/oznmon_horiz.fd)
add_subdirectory(nwprod/oznmon_shared.v2.0.0/sorc/oznmon_time.fd)
add_subdirectory(data_xtrct/sorc/make_base.fd)

Binary file added util/Ozone_Monitor/nwprod/gdas_oznmon.v2.0.0/fix/gdas_oznmon_base.tar
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2 changes: 1 addition & 1 deletion util/Ozone_Monitor/nwprod/oznmon_shared.v2.0.0/sorc/oznmon_horiz.fd/horiz.f90
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
program horiz
use read_diag
use oznmon_read_diag

implicit none
integer ntype, mls2_levs,mls3_levs
Expand Down
122 changes: 59 additions & 63 deletions ...v2.0.0/sorc/oznmon_horiz.fd/read_diag.f90 → ...sorc/oznmon_horiz.fd/oznmon_read_diag.f90
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Original file line number Diff line number Diff line change
@@ -1,27 +1,18 @@
!$$$ subprogram documentation block
! . . . .
! subprogram: read_diag read ozone diag file
! prgmmr: hliu org: np20 date: 2009-04-15
! subprogram: oznmon_read_diag read ozone diag file
!
! abstract: This module contains code to process ozone
! diagnostic files. The module defines structures
! to contain information from the ozone
! diagnostic files and then provides two routines
! to access contents of the file.
! to access contents of the file. Both binary
! and NetCDF formats are supported.
!
! program history log:
!
! contains
! read_ozndiag_header - read ozone diagnostic file header
! read_ozndiag_data - read ozone diagnostic file data
! set_netcdf_read - call set_netcdf_read(.true.) to use nc4 hooks,
! otherwise read file as binary format
! open_ozndiag - open a diag file for reading
! close_ozndiag - close an open diag file
!------------------------------------------------------------
!

module read_diag

module oznmon_read_diag

!--- use ---!

Expand Down Expand Up @@ -299,19 +290,19 @@ subroutine read_ozndiag_header( ftin, header_fix, header_nlev, new_hdr, istatus
call read_ozndiag_header_bin( ftin, header_fix, header_nlev, new_hdr, istatus )
endif

print*, 'ftin = ', ftin
print*, 'header_fix%isis = ', header_fix%isis
print*, 'header_fix%id = ', header_fix%id
print*, 'header_fix%obstype = ', header_fix%obstype
print*, 'header_fix%jiter = ', header_fix%jiter
print*, 'header_fix%nlevs = ', header_fix%nlevs
print*, 'header_fix%ianldate = ', header_fix%ianldate
print*, 'header_fix%iint = ', header_fix%iint
print*, 'header_fix%ireal = ', header_fix%ireal
print*, 'header_fix%iextra = ', header_fix%iextra

print*, 'istatus = ', istatus
print*, ''
write(6,*) 'ftin = ', ftin
write(6,*) 'header_fix%isis = ', header_fix%isis
write(6,*) 'header_fix%id = ', header_fix%id
write(6,*) 'header_fix%obstype = ', header_fix%obstype
write(6,*) 'header_fix%jiter = ', header_fix%jiter
write(6,*) 'header_fix%nlevs = ', header_fix%nlevs
write(6,*) 'header_fix%ianldate = ', header_fix%ianldate
write(6,*) 'header_fix%iint = ', header_fix%iint
write(6,*) 'header_fix%ireal = ', header_fix%ireal
write(6,*) 'header_fix%iextra = ', header_fix%iextra

write(6,*) 'istatus = ', istatus
write(6,*) ''

end subroutine read_ozndiag_header

Expand Down Expand Up @@ -349,9 +340,9 @@ subroutine read_ozndiag_header_nc( ftin, header_fix, header_nlev, new_hdr, istat
!--- get global attr
!
! This may look like overkill with a check on each variable
! name, but due to the genius of the ncdiag library, a
! failure on these read operations is fatal, because, reasons
! I guess. Thus, this abundance of caution.
! name, but a failure on these nc library read operations
! is fatal. Thus, this abundance of caution verifying the
! variable exists before attempting to retreive it.
!
if( verify_var_name_nc( "date_time" ) ) then
call nc_diag_read_get_global_attr(ftin, "date_time", idate)
Expand All @@ -377,12 +368,6 @@ subroutine read_ozndiag_header_nc( ftin, header_fix, header_nlev, new_hdr, istat
write(6,*) 'WARNING: unable to read global var Observation_type from file '
end if

if( verify_var_name_nc( "Number_of_state_vars" ) ) then
call nc_diag_read_get_global_attr(ftin, "Number_of_state_vars", nsdim )
else
write(6,*) 'WARNING: unable to read global var Number_of_state_vars from file '
end if

if( verify_var_name_nc( "pobs" ) ) then
call nc_diag_read_get_global_attr(ftin, "pobs", pobs )
else
Expand All @@ -401,7 +386,6 @@ subroutine read_ozndiag_header_nc( ftin, header_fix, header_nlev, new_hdr, istat
write(6,*) 'WARNING: unable to read global var tnoise from file '
end if


!-------------------------------------------------------------------
! The Anaysis_Use_Flag in the netcdf file resides in the
! obs data rather than global (equivalent of binary file header
Expand Down Expand Up @@ -438,6 +422,8 @@ subroutine read_ozndiag_header_nc( ftin, header_fix, header_nlev, new_hdr, istat

!--- allocate if necessary

write(6,*) 'header_fix%nlevs, nlevs_last = ', header_fix%nlevs, nlevs_last

if( header_fix%nlevs /= nlevs_last )then
if( nlevs_last > 0 )then
deallocate( header_nlev )
Expand All @@ -455,8 +441,10 @@ subroutine read_ozndiag_header_nc( ftin, header_fix, header_nlev, new_hdr, istat
header_nlev(k)%iouse = iuse_flag(k)
end do

deallocate( pobs,gross,tnoise,iuse_flag )

if( allocated( pobs )) deallocate( pobs )
if( allocated( gross )) deallocate( gross )
if( allocated( tnoise )) deallocate( tnoise )
if( allocated( iuse_flag )) deallocate( iuse_flag )

end subroutine read_ozndiag_header_nc

Expand Down Expand Up @@ -511,8 +499,8 @@ subroutine read_ozndiag_header_bin( ftin, header_fix, header_nlev, new_hdr, ista

if( header_fix%ireal /= IREAL_RESERVE ) then

print *, '### ERROR: UNEXPECTED DATA RECORD FORMAT'
print *, 'ireal =', header_fix%ireal
write(6,*) '### ERROR: UNEXPECTED DATA RECORD FORMAT'
write(6,*) 'ireal =', header_fix%ireal
stop 99

endif
Expand All @@ -524,6 +512,7 @@ subroutine read_ozndiag_header_bin( ftin, header_fix, header_nlev, new_hdr, ista

!--- allocate if necessary

write(6,*) 'header_fix%nlevs, nlevs_last = ', header_fix%nlevs, nlevs_last
if( header_fix%nlevs /= nlevs_last )then
if( nlevs_last > 0 )then
deallocate( header_nlev )
Expand All @@ -545,7 +534,11 @@ subroutine read_ozndiag_header_bin( ftin, header_fix, header_nlev, new_hdr, ista
header_nlev(k)%err = err(k)
header_nlev(k)%iouse = iouse(k)
end do
deallocate (pob,grs,err,iouse)

if( allocated( pob )) deallocate( pob )
if( allocated( grs )) deallocate( grs )
if( allocated( err )) deallocate( err )
if( allocated( iouse )) deallocate( iouse )

end subroutine read_ozndiag_header_bin

Expand Down Expand Up @@ -628,7 +621,7 @@ subroutine read_ozndiag_data_nc( ftin, header_fix, data_fix, data_nlev, data_ext
logical :: test

cur_idx = ncdiag_open_id( nopen_ncdiag )

!----------------------------------------------------------
! The binary file read (the original version of the file
! read) is designed to be called in a loop, as it reads
Expand Down Expand Up @@ -715,12 +708,13 @@ subroutine read_ozndiag_data_nc( ftin, header_fix, data_fix, data_nlev, data_ext
data_fix(ii)%obstime = obstime(ii + ((ii-1)*nlevs) )
end do

deallocate( lat, lon, obstime )
if( allocated( lat )) deallocate( lat )
if( allocated( lon )) deallocate( lon )
if( allocated( obstime )) deallocate( obstime )

!---------------------------------
! load data_nlev structure
!
allocate( data_nlev( header_fix%nlevs,nrecords ) )
allocate( ozobs(nrecords) )
allocate( ozone_inv(nrecords) )
allocate( varinv(nrecords) )
Expand Down Expand Up @@ -769,23 +763,23 @@ subroutine read_ozndiag_data_nc( ftin, header_fix, data_fix, data_nlev, data_ext
! All vars used to read the file are dimensioned
! to nrecord, which is nobs * nlevs
!
do jj=0,ntobs-1
do jj=1,ntobs-1
do ii=1,header_fix%nlevs
data_nlev(ii,jj)%ozobs = ozobs( ii + (jj * nlevs) )
data_nlev(ii,jj)%ozone_inv = ozone_inv( ii + (jj * nlevs) )
data_nlev(ii,jj)%varinv = varinv( ii + (jj * nlevs) )
data_nlev(ii,jj)%sza = sza( ii + (jj * nlevs) )
data_nlev(ii,jj)%fovn = fovn( ii + (jj * nlevs) )
data_nlev(ii,jj)%toqf = toqf( ii + (jj * nlevs) )
data_nlev(ii,jj)%ozobs = ozobs( ii + ((jj-1) * nlevs) )
data_nlev(ii,jj)%ozone_inv = ozone_inv( ii + ((jj-1) * nlevs) )
data_nlev(ii,jj)%varinv = varinv( ii + ((jj-1) * nlevs) )
data_nlev(ii,jj)%sza = sza( ii + ((jj-1) * nlevs) )
data_nlev(ii,jj)%fovn = fovn( ii + ((jj-1) * nlevs) )
data_nlev(ii,jj)%toqf = toqf( ii + ((jj-1) * nlevs) )
end do
end do

deallocate( ozobs )
deallocate( ozone_inv )
deallocate( varinv )
deallocate( sza )
deallocate( fovn )
deallocate( toqf )
if( allocated( ozobs )) deallocate( ozobs )
if( allocated( ozone_inv )) deallocate( ozone_inv )
if( allocated( varinv )) deallocate( varinv )
if( allocated( sza )) deallocate( sza )
if( allocated( fovn )) deallocate( fovn )
if( allocated( toqf )) deallocate( toqf )

ncdiag_open_status(cur_idx)%nc_read = .true.

Expand Down Expand Up @@ -831,6 +825,7 @@ subroutine read_ozndiag_data_bin( ftin, header_fix, data_fix, data_nlev, data_ex
read(ftin,IOSTAT=iflag) ntobs
write(6,*) ' READ 1, ntobs, iflag = ', ntobs, iflag

write(6,*) 'header_fix%nlevs, nlevs_last = ', header_fix%nlevs, nlevs_last
if( header_fix%nlevs /= nlevs_last )then
if( nlevs_last > 0 )then
write(6,*) ' DEALLOCATING data_nlev, data_fix, data_mpi'
Expand All @@ -845,8 +840,9 @@ subroutine read_ozndiag_data_bin( ftin, header_fix, data_fix, data_nlev, data_ex
nlevs_last = header_fix%nlevs
endif

write(6,*) 'iextra_last = ', iextra_last
if (iextra_last > 0) then
deallocate (data_extra)
deallocate ( data_extra )
endif

allocate( data_extra(header_fix%iextra,ntobs) )
Expand All @@ -869,15 +865,15 @@ subroutine read_ozndiag_data_bin( ftin, header_fix, data_fix, data_nlev, data_ex
end do
end do

deallocate(tmp_extra)
if( allocated( tmp_extra )) deallocate( tmp_extra )
endif

do j=1,ntobs
data_fix(j)%lat = tmp_fix(1,j)
data_fix(j)%lon = tmp_fix(2,j)
data_fix(j)%obstime = tmp_fix(3,j)
end do
deallocate(tmp_fix)
if( allocated( tmp_fix )) deallocate( tmp_fix )

do j=1,ntobs
do i=1,header_fix%nlevs
Expand All @@ -889,7 +885,7 @@ subroutine read_ozndiag_data_bin( ftin, header_fix, data_fix, data_nlev, data_ex
data_nlev(i,j)%toqf = tmp_nlev(6,i,j)
end do
end do
deallocate(tmp_nlev)
if( allocated( tmp_nlev )) deallocate( tmp_nlev )

nlevs_last = -1

Expand Down Expand Up @@ -966,5 +962,5 @@ logical function verify_var_name_nc( test_name )
end function verify_var_name_nc


end module read_diag
end module oznmon_read_diag

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