From 10f339d21d75ec993948225a00a1c9798f0d587c Mon Sep 17 00:00:00 2001
From: Lionel GUEZ <guez@lmd.ens.fr>
Date: Mon, 2 Sep 2019 16:11:18 +0200
Subject: [PATCH] Move the inner part of overlap to `write_overlap`
Add `.cmake` files. The idea is to have a build system independent of
the environment. This allows us to have a customized version of
`ConfigureCompilerFlags.cmake` without the `-ffpe-trap=invalid`
option.
Move the inner part of procedure overlap to a separate procedure
`write_overlap`. overlap was too complex with 6 nested constructs. The
downside is that the initialization of `e` is repeated for every
non-successive overlap. If necessary, we can later add an
initialization on first entry (but an initialization at declaration is
not possible). `write_overlap` has some consistency: all the arguments
are `intent(in)`, scalars or small vectors of intrinsic type, and
`write_overlap` only writes to files. All modifications to flow are
done outside of `write_overlap`.
---
CMakeLists.txt | 11 +----
ConfigureCompilerFlags.cmake | 47 +++++++++++++++++++
FindNetCDF.cmake | 41 +++++++++++++++++
TAGS.cmake | 61 ++++++++++++++++++++++++
Tests/CMakeLists.txt | 1 +
overlap.f90 | 84 ++++++++++------------------------
write_overlap.f90 | 89 ++++++++++++++++++++++++++++++++++++
7 files changed, 265 insertions(+), 69 deletions(-)
create mode 100644 ConfigureCompilerFlags.cmake
create mode 100644 FindNetCDF.cmake
create mode 100644 TAGS.cmake
create mode 100644 write_overlap.f90
diff --git a/CMakeLists.txt b/CMakeLists.txt
index e02593a0..c1df1125 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,5 +1,6 @@
cmake_minimum_required(VERSION 3.14)
project(Detection_eddies Fortran)
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
find_path(jumble_INCLUDE_DIR jumble.mod)
find_library(jumble_LIBRARY jumble)
@@ -55,13 +56,5 @@ target_link_libraries(extraction_eddies ${contour_531_LIBRARY}
${shapelib_LIBRARY} ${geometry_LIBRARY})
include(Tests/CMakeLists.txt)
-include(ConfigureCompilerFlags)
-
-if(CMAKE_Fortran_COMPILER_ID MATCHES GNU)
- # Gfortran bug with quiet NaNs
- # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=70817
- string(REPLACE "-ffpe-trap=invalid" "" CMAKE_Fortran_FLAGS_DEBUG
- ${CMAKE_Fortran_FLAGS_DEBUG})
-endif()
-
+include(ConfigureCompilerFlags)
include(TAGS)
diff --git a/ConfigureCompilerFlags.cmake b/ConfigureCompilerFlags.cmake
new file mode 100644
index 00000000..139e87d5
--- /dev/null
+++ b/ConfigureCompilerFlags.cmake
@@ -0,0 +1,47 @@
+if(CMAKE_Fortran_COMPILER_ID MATCHES GNU)
+ # Fortran language options:
+ string(APPEND CMAKE_Fortran_FLAGS " -std=f2003")
+
+ # Error and warning options:
+ string(APPEND CMAKE_Fortran_FLAGS
+ " -fmax-errors=1 -pedantic -Wall -Wcharacter-truncation -Wunused-parameter -Wno-conversion -Wimplicit-interface -Wimplicit-procedure -Wno-integer-division")
+
+ # Debugging options:
+ set(CMAKE_Fortran_FLAGS_DEBUG "-fbacktrace -g -ffpe-trap=zero,overflow")
+ # (We cannot use -ffpe-trap=invalid because of Gfortran bug with
+ # quiet NaNs: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=70817.)
+
+ # Code generation options:
+ string(APPEND CMAKE_Fortran_FLAGS_DEBUG
+ " -fcheck=bounds,do,mem,pointer,recursion -finit-real=nan -O0")
+
+ # Optimization options:
+ set(CMAKE_Fortran_FLAGS_RELEASE -O3)
+
+ # Hardware model options:
+ string(APPEND CMAKE_Fortran_FLAGS_RELEASE " -mcmodel=medium")
+elseif(CMAKE_Fortran_COMPILER_ID MATCHES Intel)
+ # Language:
+ string(APPEND CMAKE_Fortran_FLAGS
+ " -noaltparam -stand f03 -standard-semantics -assume nostd_mod_proc_name")
+ string(APPEND CMAKE_Fortran_FLAGS_DEBUG
+ " -check bounds,format,output_conversion,pointers,stack,uninit")
+
+ # Data:
+ string(APPEND CMAKE_Fortran_FLAGS " -auto -mcmodel=medium")
+ string(APPEND CMAKE_Fortran_FLAGS_DEBUG " -init=arrays,minus_huge,snan")
+
+ # Compiler diagnostics:
+ string(APPEND CMAKE_Fortran_FLAGS
+ " -warn declarations,general,stderrors,truncated_source,uncalled,unused,usage -traceback -diag-error-limit 1")
+
+ # Optimization:
+ string(APPEND CMAKE_Fortran_FLAGS_DEBUG " -O0")
+
+ # Floating point:
+ string(APPEND CMAKE_Fortran_FLAGS_DEBUG " -fp-stack-check -fpe-all=0")
+
+ # Debug:
+ string(APPEND CMAKE_Fortran_FLAGS_DEBUG
+ " -debug full -debug-parameters all -ftrapuv")
+endif()
diff --git a/FindNetCDF.cmake b/FindNetCDF.cmake
new file mode 100644
index 00000000..05b4e84a
--- /dev/null
+++ b/FindNetCDF.cmake
@@ -0,0 +1,41 @@
+find_path(NetCDF_INCLUDE_DIR
+ NAMES netcdf.h
+ DOC "netcdf include directories")
+##mark_as_advanced(NetCDF_INCLUDE_DIR)
+
+find_library(NetCDF_LIBRARY
+ NAMES netcdf
+ DOC "netcdf library")
+##mark_as_advanced(NetCDF_LIBRARY)
+
+if (NetCDF_INCLUDE_DIR)
+ file(STRINGS "${NetCDF_INCLUDE_DIR}/netcdf_meta.h" _netcdf_version_lines
+ REGEX "#define[ \t]+NC_VERSION_(MAJOR|MINOR|PATCH|NOTE)")
+ string(REGEX REPLACE ".*NC_VERSION_MAJOR *\([0-9]*\).*" "\\1" _netcdf_version_major "${_netcdf_version_lines}")
+ string(REGEX REPLACE ".*NC_VERSION_MINOR *\([0-9]*\).*" "\\1" _netcdf_version_minor "${_netcdf_version_lines}")
+ string(REGEX REPLACE ".*NC_VERSION_PATCH *\([0-9]*\).*" "\\1" _netcdf_version_patch "${_netcdf_version_lines}")
+ string(REGEX REPLACE ".*NC_VERSION_NOTE *\"\([^\"]*\)\".*" "\\1" _netcdf_version_note "${_netcdf_version_lines}")
+ set(NetCDF_VERSION "${_netcdf_version_major}.${_netcdf_version_minor}.${_netcdf_version_patch}${_netcdf_version_note}")
+ unset(_netcdf_version_major)
+ unset(_netcdf_version_minor)
+ unset(_netcdf_version_patch)
+ unset(_netcdf_version_note)
+ unset(_netcdf_version_lines)
+endif ()
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(NetCDF
+ REQUIRED_VARS NetCDF_LIBRARY NetCDF_INCLUDE_DIR
+ VERSION_VAR NetCDF_VERSION)
+
+if (NetCDF_FOUND)
+ set(NetCDF_INCLUDE_DIRS "${NetCDF_INCLUDE_DIR}")
+ set(NetCDF_LIBRARIES "${NetCDF_LIBRARY}")
+
+ if (NOT TARGET NetCDF::NetCDF)
+ add_library(NetCDF::NetCDF UNKNOWN IMPORTED)
+ set_target_properties(NetCDF::NetCDF PROPERTIES
+ IMPORTED_LOCATION "${NetCDF_LIBRARY}"
+ INTERFACE_INCLUDE_DIRECTORIES "${NetCDF_INCLUDE_DIR}")
+ endif ()
+endif ()
diff --git a/TAGS.cmake b/TAGS.cmake
new file mode 100644
index 00000000..4cdf2953
--- /dev/null
+++ b/TAGS.cmake
@@ -0,0 +1,61 @@
+#
+# (C) Copyright 2018 Tillmann Heidsieck
+#
+# SPDX-License-Identifier: MIT
+#
+
+find_program(CTAGS ctags)
+
+function(tags_add_dir _dir)
+ get_property(_subdirlist DIRECTORY "${_dir}" PROPERTY SUBDIRECTORIES)
+ foreach(_sd ${_subdirlist})
+ tags_add_dir(${_sd})
+ endforeach()
+
+ get_property(_targets_list DIRECTORY "${_dir}" PROPERTY
+ BUILDSYSTEM_TARGETS)
+ foreach(_tgt ${_targets_list})
+ get_property(_t_files TARGET ${_tgt} PROPERTY SOURCES)
+ list(FILTER _t_files EXCLUDE REGEX TARGET_OBJECTS)
+ get_property(_t_defs TARGET ${_tgt} PROPERTY
+ COMPILE_DEFINITIONS)
+
+ list(APPEND _all_source_files ${_t_files})
+ string(REGEX REPLACE "${CMAKE_SOURCE_DIR}/" "" _t_files
+ "${_t_files}")
+ string(REGEX REPLACE ";" "\n" _t_files "${_t_files}")
+
+ string(REGEX REPLACE ";" "\n" _t_defs "${_t_defs}")
+ string(REGEX REPLACE "^([^=]+)$" "\\1=1" _t_defs "${_t_defs}")
+ endforeach()
+ set(_all_source_files ${_all_source_files} PARENT_SCOPE)
+ set(_all_definitions ${_all_definitions} PARENT_SCOPE)
+endfunction()
+
+if(CTAGS)
+ set(SOURCES_LIST "${CMAKE_BINARY_DIR}/sources_list")
+ set(_all_source_files "")
+ set(_all_definitions "")
+
+ file(REMOVE "${SOURCES_LIST}")
+
+ tags_add_dir(${CMAKE_SOURCE_DIR})
+
+ list(SORT _all_source_files)
+ list(REMOVE_DUPLICATES _all_source_files)
+ string(REGEX REPLACE "${CMAKE_SOURCE_DIR}/" "" _asf
+ "${_all_source_files}")
+ string(REGEX REPLACE ";" "\n" _asf "${_asf}")
+ file(APPEND ${SOURCES_LIST} "\n${_asf}")
+
+ string(REGEX REPLACE ";" "\n" _all_definitions "${_all_definitions}")
+ string(REGEX REPLACE "^([^=]+)$" "\\1=1" _all_definitions
+ "${_all_definitions}")
+
+ add_custom_target(TAGS DEPENDS ${CMAKE_SOURCE_DIR}/TAGS)
+ add_custom_command(OUTPUT ${CMAKE_SOURCE_DIR}/TAGS
+ COMMAND ctags -e --language-force=fortran -L ${SOURCES_LIST}
+ DEPENDS ${_all_source_files}
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+ VERBATIM)
+endif()
diff --git a/Tests/CMakeLists.txt b/Tests/CMakeLists.txt
index 6a8a3c1d..386ae43e 100644
--- a/Tests/CMakeLists.txt
+++ b/Tests/CMakeLists.txt
@@ -33,6 +33,7 @@ add_executable(test_successive_overlap derived_types.f90 overlap.f90
read_snapshot.f90 spher_polygon_area.f90 spher_polyline_area.f90
weight.f90 read_eddy.f90 read_field_indices.f90
candidate_overlap.f90 write_eddy.f90 init_shapefiles.f90
+ write_overlap.f90
${CMAKE_CURRENT_LIST_DIR}/test_successive_overlap.f90)
target_include_directories(test_successive_overlap PRIVATE
diff --git a/overlap.f90 b/overlap.f90
index bbcae6a4..900d53d6 100644
--- a/overlap.f90
+++ b/overlap.f90
@@ -7,23 +7,25 @@ contains
subroutine overlap(flow, unit_edgelist, nlon, nlat, periodic, dist_lim, &
hshp_extremum, hshp_outermost, hshp_max_speed, j, k, delta)
- ! Finds edges between flow(j - delta) and flow(j), corresponding to
- ! dates k - delta and k. Writes these edges to unit_edgelist. Updates
- ! flow(j - delta)%list_vis%delta_out and flow(j)%list_vis%delta_in.
+ ! Finds edges between flow(j - delta) and flow(j), corresponding
+ ! to dates k - delta and k. Calls write_overlap for these
+ ! edges. Updates flow(j - delta)%list_vis%delta_out,
+ ! flow(j)%list_vis%delta_in and flow(j - delta + 1:j -
+ ! 1)%number_eddies.
! Libraries:
use contour_531, only: polyline
use gpc_f, only: gpc_polygon_clip_f, GPC_INT, polygon
use nr_util, only: twopi
+ use shapelib, only: shpfileobject
use candidate_overlap_m, only: candidate_overlap
- use derived_types, only: snapshot, eddy, null_ssh_contour, missing_speed
+ use derived_types, only: snapshot
use interpolate_eddy_m, only: interpolate_eddy
- use shapelib, only: shpfileobject
use spher_polygon_area_m, only: spher_polygon_area
use spher_polyline_area_m, only: spher_polyline_area
use weight_m, only: weight
- use write_eddy_m, only: write_eddy
+ use write_overlap_m, only: write_overlap
type(snapshot), intent(inout):: flow(:) ! (max_delta + 1)
integer, intent(in):: unit_edgelist ! logical unit for edgelist file
@@ -49,11 +51,9 @@ contains
! Local:
- integer i1, i2, l, n_select, m, i_pred, j_interp, k_interp
+ integer i1, i2, l, n_select, m
type(polyline) polyline_1, polyline_2
type(polygon) res_pol
- real w, w_interp, coord_extr_2(2)
- type(eddy) e
integer, allocatable:: selection(:)
! identifying numbers of a selection of extrema
@@ -64,16 +64,6 @@ contains
!-----------------------------------------------------------------------
- if (delta >= 2) then
- ! Set some null components of the interpolated eddy:
- e%out_cont = null_ssh_contour()
- e%speed_cont = null_ssh_contour()
- e%max_speed = missing_speed
- e%valid = .false.
- e%interpolated = .true.
- e%radius4 = 0
- end if
-
do i1 = 1, flow(j - delta)%number_vis_extr
if (flow(j - delta)%list_vis(i1)%valid) then
! Define the geographical window around each eddy extremum:
@@ -121,47 +111,21 @@ contains
if (spher_polygon_area(res_pol) >= 0.25 &
* min(spher_polyline_area(polyline_1), &
spher_polyline_area(polyline_2))) then
- w = weight(flow(j - delta)%list_vis(i1), &
- flow(j)%list_vis(i2))
- i_pred = i1
-
- if (delta >= 2) then
- ! Prepare interpolation:
-
- e%cyclone = flow(j - delta)%list_vis(i1)%cyclone
-
- ! Define coord_extr_2 with the longitude of
- ! extremum i2 shifted to a value close to the
- ! longitude of extremum i1:
- coord_extr_2(1) = flow(j)%list_vis(i2)%coord_extr(1) &
- + m * twopi
- coord_extr_2(2) = flow(j)%list_vis(i2)%coord_extr(2)
- end if
-
- do j_interp = j - delta + 1, j - 1
- ! Count one more fictitious eddy at j_interp:
- flow(j_interp)%number_eddies &
- = flow(j_interp)%number_eddies + 1
-
- ! Interpolate extremum:
- w_interp = (j_interp - j + delta) / real(delta)
- e%coord_extr = (1 - w_interp) &
- * flow(j - delta)%list_vis(i1)%coord_extr &
- + w_interp * coord_extr_2
- e%ssh_extr = (1 - w_interp) &
- * flow(j - delta)%list_vis(i1)%ssh_extr + w_interp &
- * flow(j)%list_vis(i2)%ssh_extr
-
- k_interp = k - j + j_interp
- call write_eddy(e, hshp_extremum, hshp_outermost, &
- hshp_max_speed, k_interp, &
- flow(j_interp)%number_eddies)
- write(unit_edgelist, fmt = *) k_interp - 1, i_pred, &
- k_interp, flow(j_interp)%number_eddies, w
- i_pred = flow(j_interp)%number_eddies
- end do
-
- write(unit_edgelist, fmt = *) k - 1, i_pred, k, i2, w
+ ! Count one more fictitious eddy between j - delta
+ ! + 1 and j - 1:
+ flow(j - delta + 1:j - 1)%number_eddies &
+ = flow(j - delta + 1:j - 1)%number_eddies + 1
+
+ call write_overlap(k, delta, i1, i2, &
+ flow(j - delta + 1:j - 1)%number_eddies, &
+ flow(j - delta)%list_vis(i1)%cyclone, &
+ flow(j - delta)%list_vis(i1)%coord_extr, &
+ flow(j - delta)%list_vis(i1)%ssh_extr, &
+ flow(j)%list_vis(i2)%coord_extr, &
+ flow(j)%list_vis(i2)%ssh_extr, m, hshp_extremum, &
+ hshp_outermost, hshp_max_speed, unit_edgelist, &
+ weight(flow(j - delta)%list_vis(i1), &
+ flow(j)%list_vis(i2)))
flow(j - delta)%list_vis(i1)%delta_out = delta
flow(j)%list_vis(i2)%delta_in = delta
end if
diff --git a/write_overlap.f90 b/write_overlap.f90
new file mode 100644
index 00000000..69d570dc
--- /dev/null
+++ b/write_overlap.f90
@@ -0,0 +1,89 @@
+module write_overlap_m
+
+ implicit none
+
+contains
+
+ subroutine write_overlap(k, delta, i1, i2, i_interp, cyclone, coord_extr_1, &
+ ssh_extr_1, coord_extr_2, ssh_extr_2, m, hshp_extremum, hshp_outermost, &
+ hshp_max_speed, unit_edgelist, w)
+
+ ! Libraries:
+ use nr_util, only: twopi
+ use shapelib, only: shpfileobject
+
+ use derived_types, only: eddy, null_ssh_contour, missing_speed
+ use write_eddy_m, only: write_eddy
+
+ integer, intent(in):: k ! date index
+ integer, intent(in):: delta
+ integer, intent(in):: i1
+ integer, intent(in):: i2
+ integer, intent(in):: i_interp(:) ! (delta - 1)
+ logical, intent(in):: cyclone
+ real, intent(in):: coord_extr_1(:) ! (2)
+ real, intent(in):: ssh_extr_1
+
+ real, intent(in):: coord_extr_2(:) ! (2)
+ ! (Note: value attribute not allowed for an array.)
+
+ real, intent(in):: ssh_extr_2
+ integer, intent(in):: m
+ TYPE(shpfileobject), intent(in):: hshp_extremum ! shapefile extremum
+
+ TYPE(shpfileobject), intent(in):: hshp_outermost
+ ! shapefile outermost_contour
+
+ TYPE(shpfileobject), intent(in):: hshp_max_speed ! shapefile x_speed_contour
+ integer, intent(in):: unit_edgelist ! logical unit for edgelist file
+ real, intent(in):: w
+
+ ! Local:
+ type(eddy) e
+ integer i_pred, j_interp, k_interp
+ real w_interp
+ real coord_extr_2_local(2)
+
+ !-------------------------------------------------------------------
+
+ if (delta >= 2) then
+ ! Set some null components of the interpolated eddy:
+ e%out_cont = null_ssh_contour()
+ e%speed_cont = null_ssh_contour()
+ e%max_speed = missing_speed
+ e%valid = .false.
+ e%interpolated = .true.
+ e%radius4 = 0
+
+ ! Prepare interpolation:
+
+ e%cyclone = cyclone
+
+ ! Define coord_extr_2_local with the longitude of extremum i2 shifted
+ ! to a value close to the longitude of extremum i1:
+ coord_extr_2_local(1) = coord_extr_2(1) + m * twopi
+ coord_extr_2_local(2) = coord_extr_2(2)
+ end if
+
+ i_pred = i1
+
+ do j_interp = 1, delta - 1
+ ! Interpolate extremum:
+ w_interp = j_interp / real(delta)
+ e%coord_extr = (1 - w_interp) * coord_extr_1 &
+ + w_interp * coord_extr_2_local
+ e%ssh_extr = (1 - w_interp) * ssh_extr_1 + w_interp * ssh_extr_2
+
+ k_interp = k - delta + j_interp
+ call write_eddy(e, hshp_extremum, hshp_outermost, hshp_max_speed, &
+ k_interp, i_interp(j_interp))
+ write(unit_edgelist, fmt = *) k_interp - 1, i_pred, k_interp, &
+ i_interp(j_interp), w
+ i_pred = i_interp(j_interp)
+ end do
+
+ write(unit_edgelist, fmt = *) k - 1, i_pred, k, i2, w
+
+ end subroutine write_overlap
+
+end module write_overlap_m
--
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