Polish

ConfigureCompilerFlags.cmake

 if(CMAKE_Fortran_COMPILER_ID MATCHES GNU)
+  # Options for a Fortran 2003 program, compiler version 7
+  
   # Fortran language options:
   string(APPEND CMAKE_Fortran_FLAGS " -std=f2003")
 
@@ -7,7 +9,8 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES GNU)
     " -fmax-errors=1 -pedantic -Wall -Wcharacter-truncation -Wunused-parameter"
     " -Wno-conversion -Wimplicit-interface -Wimplicit-procedure"
     " -Wno-integer-division -Wno-maybe-uninitialized")
-
+  ## -Wrealloc-lhs-all
+  
   # Debugging options:
   set(CMAKE_Fortran_FLAGS_DEBUG "-fbacktrace -g -ffpe-trap=zero,overflow")
   # (We cannot use -ffpe-trap=invalid because of Gfortran bug with
@@ -25,10 +28,17 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES GNU)
   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")
+  # -standard-semantics by itself implies -assume std_mod_proc_name, and
+  # then compiling with the NetCDF Fortran library or the FortranGIS
+  # library might not work.
+  
   string(APPEND CMAKE_Fortran_FLAGS_DEBUG
     " -check bounds,format,output_conversion,pointers,stack,uninit")
+  # "-check all" includes "arg_temp_created", which is annoying so we
+  # detail "check bounds", etc.
 
   # Data:
 
@@ -46,6 +56,7 @@ elseif(CMAKE_Fortran_COMPILER_ID MATCHES Intel)
   string(APPEND CMAKE_Fortran_FLAGS
     " -warn declarations,general,stderrors,truncated_source,uncalled,unused,usage"
     " -traceback -diag-error-limit 1")
+  # -traceback has no impact on run-time execution speeds.
   
   # Optimization:
   string(APPEND CMAKE_Fortran_FLAGS_DEBUG " -O0")
@@ -58,5 +69,9 @@ elseif(CMAKE_Fortran_COMPILER_ID MATCHES Intel)
     " -debug full -debug-parameters all -ftrapuv")
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES NAG)
   string(APPEND CMAKE_Fortran_FLAGS " -f2003")
+
   string(APPEND CMAKE_Fortran_FLAGS_DEBUG " -C=all -gline -nan -strict95")
+  #  -C=undefined is not binary compatible with Fortran code compiled
+  #  without that option, and is not compatible with calling C code
+  #  via a BIND(C) interface.
 endif()

FindNetCDF.cmake

@@ -65,6 +65,10 @@ if (PkgConfig_FOUND)
   pkg_check_modules(_NetCDF QUIET netcdf IMPORTED_TARGET)
   if (_NetCDF_FOUND)
     unset(netCDF_DIR CACHE)
+    pkg_get_variable(netcdf_pcfiledir netcdf pcfiledir)
+    message(STATUS "${CMAKE_CURRENT_LIST_FILE}")
+    message(STATUS "-- Location of .pc file: ${netcdf_pcfiledir}")
+    message(STATUS "-- NetCDF include directories: ${_NetCDF_INCLUDE_DIRS}")
     message(STATUS "-- NetCDF libraries: ${_NetCDF_LINK_LIBRARIES}")
     # Forward the variables in a consistent way.
     set(NetCDF_FOUND "${_NetCDF_FOUND}")

FindNetCDF_Fortran.cmake

 find_package(PkgConfig REQUIRED)
 pkg_check_modules(NetCDF_Fortran REQUIRED IMPORTED_TARGET netcdf-fortran)
+pkg_get_variable(netcdf_fortran_pcfiledir netcdf-fortran pcfiledir)
+message(STATUS "${CMAKE_CURRENT_LIST_FILE}")
+message(STATUS "-- Location of .pc file: ${netcdf_fortran_pcfiledir}")
 
 message(STATUS
-  "-- NetCDF-Fortran include flags: ${NetCDF_Fortran_INCLUDE_DIRS}")
+  "-- NetCDF-Fortran include directories: ${NetCDF_Fortran_INCLUDE_DIRS}")
 
 message(STATUS "-- NetCDF-Fortran libraries: ${NetCDF_Fortran_LINK_LIBRARIES}")
 

Inst_eddies/inst_eddies.py

@@ -10,7 +10,9 @@ import subprocess
 import shapefile
 
 parser = argparse.ArgumentParser()
-parser.add_argument("first_file")
+parser.add_argument("first_file",
+                    help = "NetCDF file containing SSH and velocity at a "
+                    "single date")
 parser.add_argument("-l", "--last_date", help = "%%Y-%%m-%%d")
 parser.add_argument("-b", "--bbox", nargs=4, type = float,
                     metavar = ("xmin", "xmax", "ymin", "ymax"))

Overlap/Tests/test_overlap.f90

@@ -88,10 +88,12 @@ program test_overlap
   call read_snapshot(flow(max_delta + 1), k_test_2, hshp, corner, step, nlon, &
        nlat, copy, k1, ishape_last)
   CALL shp_tr_close(hshp)
-  print *, "Enter flow(1)%list_vis%delta_out (array):"
+  print *, "Enter flow(1)%list_vis%delta_out (array with ", &
+       flow(1)%number_vis_extr, " values):"
   read *, flow(1)%list_vis%delta_out
   print *, "flow(1)%list_vis%delta_out:", flow(1)%list_vis%delta_out
-  print *, "Enter flow(max_delta + 1)%list_vis%delta_in (array):"
+  print *, "Enter flow(max_delta + 1)%list_vis%delta_in (array with ", &
+       flow(max_delta + 1)%number_vis_extr, " values)):"
   read *, flow(max_delta + 1)%list_vis%delta_in
   print *, "flow(max_delta + 1)%list_vis%delta_in:", &
        flow(max_delta + 1)%list_vis%delta_in