Merge branch 'relax_coord_bound' of https://github.com/wkliao/netcdf-…

…fortran into pr-aggregation.wif

.travis.yml

@@ -12,11 +12,11 @@ services:
 
 env:
     matrix:
-        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-fsigned-char' CURHOST=docker-nc3-gcc-x64-signed
-        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-fsigned-char' CURHOST=docker-nc3-gcc-x86-signed
+        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   COPTS='-DENABLE_NETCDF4=OFF -DCMAKE_C_FLAGS=-fsigned-char' CURHOST=docker-nc3-gcc-x64-signed
+        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   COPTS='-DENABLE_NETCDF4=OFF -DCMAKE_C_FLAGS=-fsigned-char' CURHOST=docker-nc3-gcc-x86-signed
 
-        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-funsigned-char' CURHOST=docker-nc3-gcc-x64-unsigned
-        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-funsigned-char' CURHOST=docker-nc3-gcc-x86-unsigned
+        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   COPTS='-DENABLE_NETCDF4=OFF -DCMAKE_C_FLAGS=-funsigned-char' CURHOST=docker-nc3-gcc-x64-unsigned
+        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   COPTS='-DENABLE_NETCDF4=OFF -DCMAKE_C_FLAGS=-funsigned-char' CURHOST=docker-nc3-gcc-x86-unsigned
 
         - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   COPTS='-DCMAKE_C_FLAGS=-fsigned-char' CURHOST=docker-nc4-gcc-x64-signed
         - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   COPTS='-DCMAKE_C_FLAGS=-fsigned-char' CURHOST=docker-nc4-gcc-x86-signed

CMakeExtras/Makefile.am

@@ -1 +1,3 @@
-EXTRA_DIST = sizeof_ptrdiff_t.c test_c_ptrdiff_t.f90 MatchNetCDFFortranTypes.cmake
+EXTRA_DIST = sizeof_ptrdiff_t.c test_c_ptrdiff_t.f90 \
+             MatchNetCDFFortranTypes.cmake \
+             check_relax_coord_bound.c check_pnetcdf.c check_parallel4.c

CMakeExtras/check_parallel4.c

@@ -0,0 +1,6 @@
+#include <netcdf_meta.h>
+#if !defined(NC_HAS_PARALLEL4) || NC_HAS_PARALLEL4 == 0
+      choke me
+#endif
+int main() {return 0;}
+

CMakeExtras/check_pnetcdf.c

@@ -0,0 +1,5 @@
+#include <netcdf_meta.h>
+#if !defined(NC_HAS_PNETCDF) || NC_HAS_PNETCDF == 0
+      choke me
+#endif
+int main() {return 0;}

CMakeExtras/check_relax_coord_bound.c

@@ -0,0 +1,5 @@
+#include <netcdf_meta.h>
+#if !defined(NC_RELAX_COORD_BOUND) || NC_RELAX_COORD_BOUND == 0
+      choke me
+#endif
+int main() {return 0;}

CMakeLists.txt

@@ -287,7 +287,10 @@ MACRO(print_conf_summary)
     MESSAGE(STATUS "\tUsing pnetcdf:\t\t\t" ${STATUS_PNETCDF})
   ENDIF(STATUS_PNETCDF)
 
-  MESSAGE(STATUS "\tUsing Parallel IO:\t\t" ${STATUS_PARALLEL})
+  MESSAGE(STATUS "\tBuilding Parallel IO:\t\t" ${BUILD_PARALLEL})
+  MESSAGE(STATUS "\tUsing NetCDF4 Parallel IO:\t" ${NF_HAS_PARALLEL4})
+  MESSAGE(STATUS "\tUsing PnetCDF Parallel IO:\t" ${NF_HAS_PNETCDF})
+  MESSAGE(STATUS "\tTesting Parallel IO:\t\t" ${TEST_PARALLEL})
 
   IF(CMAKE_PREFIX_PATH)
     MESSAGE(STATUS "\tCMake Prefix Path:\t\t" "${CMAKE_PREFIX_PATH}")
@@ -393,37 +396,28 @@ IF(ENABLE_PARALLEL_TESTS)
 ENDIF()
 
 ###
-# Seek out dependent libraries.
+# Seek out netcdf library file and include path.
 ###
 
-IF(NOT netCDF_LIBRARIES AND NOT netCDF_INCLUDE_DIR)
-  FIND_PACKAGE(netCDF)
-ELSE()
-  SET(netCDF_FOUND TRUE)
+IF(NOT NETCDF_C_LIBRARY)
+  FIND_LIBRARY(NETCDF_C_LIBRARY NAMES netcdf)
+  IF(NOT NETCDF_C_LIBRARY)
+    MESSAGE(FATAL_ERROR "libnetcdf not found.")
+  ENDIF()
 ENDIF()
+MESSAGE(STATUS "Found netcdf library: ${NETCDF_C_LIBRARY}")
 
-IF (netCDF_FOUND)
-  INCLUDE_DIRECTORIES(SYSTEM ${netCDF_INCLUDE_DIR})
-  SET(NETCDF_C_LIBRARY ${netCDF_LIBRARIES})
-  SET(NETCDF_C_INCLUDE_DIR ${netCDF_INCLUDE_DIR})
-ELSE()
-  # netCDF not properly packaged. Try to find it manually.
-  FIND_LIBRARY(NETCDF_C_LIBRARY NAMES netcdf libnetcdf)
-  IF(NOT NETCDF_C_LIBRARY)
-    MESSAGE(FATAL_ERROR "libnetcdf not found. Please reinstall and try again.")
-  ELSE()
-    MESSAGE(STATUS "Found netcdf: ${NETCDF_C_LIBRARY}")
-    FIND_PATH(NC_H_INCLUDE_DIR "netcdf.h")
-    IF(NOT NC_H_INCLUDE_DIR)
-      MESSAGE(FATAL_ERROR "Directory containing netcdf.h cannot be found. Please reinstall and try again.")
-    ELSE()
-      INCLUDE_DIRECTORIES(SYSTEM ${NC_H_INCLUDE_DIR})
-    ENDIF()
+IF(NOT NETCDF_INCLUDE_DIR)
+  FIND_PATH(NETCDF_INCLUDE_DIR NAMES netcdf.h)
+  IF(NOT NETCDF_INCLUDE_DIR)
+    MESSAGE(FATAL_ERROR "netcdf.h not found.")
   ENDIF()
 ENDIF()
+MESSAGE(STATUS "Found netcdf.h in ${NETCDF_INCLUDE_DIR}")
+INCLUDE_DIRECTORIES(SYSTEM ${NETCDF_INCLUDE_DIR})
 
 ###
-# End 'seek out dependent libraries'
+# End 'Seek out netcdf library file and include path.'
 ###
 
 ###
@@ -520,7 +514,6 @@ CHECK_LIBRARY_EXISTS(${NETCDF_C_LIBRARY} nc_def_opaque "" USE_NETCDF4)
 CHECK_LIBRARY_EXISTS(${NETCDF_C_LIBRARY} nccreate "" USE_NETCDF_V2)
 CHECK_LIBRARY_EXISTS(${NETCDF_C_LIBRARY} nc_set_log_level "" USE_LOGGING)
 CHECK_LIBRARY_EXISTS(${NETCDF_C_LIBRARY} oc_open "" BUILD_DAP)
-CHECK_LIBRARY_EXISTS(${NETCDF_C_LIBRARY} nc_use_parallel_enabled "" BUILD_PARALLEL)
 
 IF(USE_NETCDF4)
   SET(NC_BUILD_V4 TRUE)
@@ -531,24 +524,18 @@ IF(USE_NETCDF_V2)
   SET(HAVE_NCCREATE TRUE)
 ENDIF(USE_NETCDF_V2)
 
+SET(STATUS_LOGGING OFF)
 IF(USE_LOGGING)
   SET(HAVE_NC_SET_LOG_LEVEL TRUE)
   SET(STATUS_LOGGING ON)
 ENDIF(USE_LOGGING)
 
+SET(ENABLE_DAP OFF)
 IF(BUILD_DAP)
   SET(HAVE_OC_OPEN TRUE)
   SET(ENABLE_DAP ON)
 ENDIF(BUILD_DAP)
 
-IF(BUILD_PARALLEL)
-  SET(STATUS_PARALLEL ON)
-  SET(HAVE_NC_USE_PARALLEL_ENABLED TRUE)
-  FIND_PATH(NC_MPIF_H_PATH "mpif.h")
-  IF(NC_MPIF_H_PATH)
-    INCLUDE_DIRECTORIES(${NC_MPIF_H_PATH})
-  ENDIF(NC_MPIF_H_PATH)
-ENDIF(BUILD_PARALLEL)
 ##
 # Set some status messages for the summary.
 ##
@@ -558,10 +545,10 @@ ENDIF(BUILD_PARALLEL)
 # End status messages/variables.
 ##
 
+SET(ENABLE_NETCDF4 OFF)
 IF(USE_NETCDF4)
   SET(ENABLE_NETCDF4 ON)
   ADD_DEFINITIONS(-DUSE_NETCDF4)
-  SET(ENABLE_NETCDF_4 ON CACHE BOOL "")
   SET(ENABLE_NETCDF4 ON CACHE BOOL "")
 ENDIF()
 
@@ -573,6 +560,40 @@ IF (UNIX AND ${CMAKE_SIZEOF_VOID_P} MATCHES "8")
   endif ()
 ENDIF()
 
+# Determine C library setting for NC_RELAX_COORD_BOUND
+try_compile(NF_RELAX_COORD_BOUND ${CMAKE_CURRENT_BINARY_DIR}
+  "${CMAKE_CURRENT_SOURCE_DIR}/CMakeExtras/check_relax_coord_bound.c"
+  CMAKE_FLAGS "-DINCLUDE_DIRECTORIES=${NETCDF_INCLUDE_DIR}"
+  )
+
+# Determine C library setting for NC_HAS_PNETCDF
+try_compile(NF_HAS_PNETCDF ${CMAKE_CURRENT_BINARY_DIR}
+  "${CMAKE_CURRENT_SOURCE_DIR}/CMakeExtras/check_pnetcdf.c"
+  CMAKE_FLAGS "-DINCLUDE_DIRECTORIES=${NETCDF_INCLUDE_DIR}"
+  )
+
+# Determine C library setting for NC_HAS_PARALLEL4
+try_compile(NF_HAS_PARALLEL4 ${CMAKE_CURRENT_BINARY_DIR}
+  "${CMAKE_CURRENT_SOURCE_DIR}/CMakeExtras/check_parallel4.c"
+  CMAKE_FLAGS "-DINCLUDE_DIRECTORIES=${NETCDF_INCLUDE_DIR}"
+  )
+
+IF(NF_HAS_PARALLEL4)
+  ADD_DEFINITIONS(-DNF_HAS_PARALLEL4)
+ENDIF()
+IF(NF_HAS_PNETCDF)
+  ADD_DEFINITIONS(-DNF_HAS_PNETCDF)
+ENDIF()
+
+IF(NF_HAS_PNETCDF OR NF_HAS_PARALLEL4)
+  SET(BUILD_PARALLEL ON)
+  SET(HAVE_NC_USE_PARALLEL_ENABLED TRUE)
+ELSE(NF_HAS_PNETCDF OR NF_HAS_PARALLEL4)
+  SET(BUILD_PARALLEL OFF)
+  SET(HAVE_NC_USE_PARALLEL_ENABLED FALSE)
+  SET(TEST_PARALLEL OFF)
+ENDIF(NF_HAS_PNETCDF OR NF_HAS_PARALLEL4)
+
 # Determine C/Fortran pointer compatibility.
 try_compile(COMPILE_SUCCESS ${CMAKE_CURRENT_BINARY_DIR}
   "${CMAKE_CURRENT_SOURCE_DIR}/CMakeExtras/test_c_ptrdiff_t.f90"
@@ -623,7 +644,7 @@ IF(ENABLE_FORTRAN_TYPE_CHECKS)
   # Do tests to determine which Fortran types correspond to NCBYTE, NCSHORT, ...
   # The configure file got these by testing an F77 program, invoking
   # UD_FORTRAN_TYPES defined in acinclude.m4.
-  
+
   INCLUDE(CMakeExtras/MatchNetCDFFortranTypes.cmake)
 ELSE()
   # Set Fortran types to default.
@@ -714,8 +735,8 @@ IF(NC_EXTRA_DEPS)
   FOREACH(_DEP ${DEPS_LIST})
     STRING(REGEX REPLACE "^-l" "" _LIB ${_DEP})
     FIND_LIBRARY("${_LIB}_DEP" NAMES "${_LIB}" "lib${_LIB}")
-    MESSAGE(${${_LIB}_DEP})
-    IF(NOT "${_LIB}_DEP")
+    # MESSAGE(${${_LIB}_DEP})
+    IF(${_LIB}_DEP STREQUAL "")
       MESSAGE(FATAL_ERROR "Error finding ${_LIB}.")
     ELSE()
       MESSAGE(STATUS "Found ${_LIB}: ${${_LIB}_DEP}")

configure.ac

@@ -35,6 +35,33 @@ AC_CONFIG_SRCDIR([libsrc/fort-attio.c])
 
 AC_MSG_NOTICE([checking user options])
 
+AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[
+#include <netcdf_meta.h>
+#if !defined(NC_RELAX_COORD_BOUND) || NC_RELAX_COORD_BOUND == 0
+      choke me
+#endif]])], [nc_relax_coord_bound=yes], [nc_relax_coord_bound=no])
+if test "x$nc_relax_coord_bound" = xyes; then
+   AC_DEFINE([NF_RELAX_COORD_BOUND], [1], [Enable a more relaxed boundary error check NF_EINVALCOORDS])
+fi
+
+AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[
+#include <netcdf_meta.h>
+#if !defined(NC_HAS_PNETCDF) || NC_HAS_PNETCDF == 0
+      choke me
+#endif]])], [nc_has_pnetcdf=yes], [nc_has_pnetcdf=no])
+if test "x$nc_has_pnetcdf" = xyes; then
+   AC_DEFINE([NF_HAS_PNETCDF], [1], [Enable parallel I/O support via PnetCDF])
+fi
+
+AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[
+#include <netcdf_meta.h>
+#if !defined(NC_HAS_PARALLEL4) || NC_HAS_PARALLEL4 == 0
+      choke me
+#endif]])], [nc_has_parallel4=yes], [nc_has_parallel4=no])
+if test "x$nc_has_parallel4" = xyes; then
+   AC_DEFINE([NF_HAS_PARALLEL4], [1], [Enable parallel I/O support via HDF5])
+fi
+
 # Does the user want to run extra tests with valgrind?
 AC_MSG_CHECKING([whether extra valgrind tests should be run])
 AC_ARG_ENABLE([valgrind-tests],
@@ -51,6 +78,10 @@ AC_ARG_ENABLE([parallel-tests],
                                netCDF-4 is not enabled, or built on a system \
                                without parallel I/O support.])])
 test "x$enable_parallel_tests" = xyes || enable_parallel_tests=no
+if test "x$nc_has_pnetcdf" = xno -a "x$nc_has_parallel4" = xno ; then
+   # paralle I/O is not enabled
+   enable_parallel_tests=no
+fi
 AC_MSG_RESULT($enable_parallel_tests)
 
 # Does the user want to do some extra tests?
@@ -462,7 +493,7 @@ AC_CHECK_HEADERS([netcdf.h], [], [AC_MSG_ERROR([netcdf.h could not be found. Ple
 AC_SEARCH_LIBS([nc_open], [netcdf])
 
 # See if various libraries are available
-AC_CHECK_FUNCS([nc_def_opaque nccreate nc_set_log_level oc_open nc_use_parallel_enabled])
+AC_CHECK_FUNCS([nc_def_opaque nccreate nc_set_log_level oc_open])
 #test "x$ac_cv_func_oc_open" = xyes && nc_has_dap=yes || nc_has_dap=no
 # Whether we build/test some functionality depends on what we found in
 # the C library.
@@ -473,19 +504,16 @@ nc_build_v2=no
 nc_build_v4=no
 nc_has_logging=no
 nc_has_dap=no
-nc_has_parallel=no
 
 test "x$ac_cv_func_nc_def_opaque" = xyes && nc_build_v4=yes
 test "x$ac_cv_func_nccreate" = xyes && nc_build_v2=yes
 test "x$ac_cv_func_nc_set_log_level" = xyes && nc_has_logging=yes
 test "x$ac_cv_func_oc_open" = xyes && nc_has_dap=yes
-test "x$ac_cv_func_nc_use_parallel_enabled" = xyes && nc_has_parallel=yes
 
 #AC_CHECK_FUNC([nc_def_opaque],[nc_build_v4=yes])
 #AC_CHECK_FUNC([nccreate],[nc_build_v2=yes])
 #AC_CHECK_FUNC([nc_set_log_level],[nc_has_logging=yes])
 #AC_CHECK_FUNC([oc_open],[nc_has_dap=yes])
-#AC_CHECK_FUNC([nc_use_parallel_enabled],[nc_has_parallel=yes])
 
 if test "x$nc_build_v4" = xyes; then
    AC_DEFINE([USE_NETCDF4], [1], [if true, build netCDF-4])
@@ -500,7 +528,9 @@ AM_CONDITIONAL([USE_NETCDF4], [test "x$nc_build_v4" = xyes])
 AM_CONDITIONAL([BUILD_V2], [test "x$nc_build_v2" = xyes])
 AM_CONDITIONAL([USE_LOGGING], [test "x$nc_has_logging" = xyes])
 AM_CONDITIONAL([BUILD_DAP], [test "x$nc_has_dap" = xyes])
-AM_CONDITIONAL([BUILD_PARALLEL], [test "x$nc_has_parallel" = xyes])
+AM_CONDITIONAL([BUILD_PNETCDF], [test "x$nc_has_pnetcdf" = xyes])
+AM_CONDITIONAL([BUILD_PARALLEL4], [test "x$nc_has_parallel4" = xyes])
+AM_CONDITIONAL([BUILD_PARALLEL], [test "x$nc_has_pnetcdf" = xyes -o "x$nc_has_parallel4" = xyes])
 AC_CHECK_HEADER(stdlib.h, ,AC_DEFINE([NO_STDLIB_H], [], [no stdlib.h]))
 AC_CHECK_HEADER(sys/types.h, ,AC_DEFINE([NO_SYS_TYPES_H], [], [no sys_types.h]))
 AC_CHECK_HEADERS([sys/param.h])

fortran/CMakeLists.txt

@@ -1,6 +1,6 @@
 CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
 
-SET(CMAKE_VERBOSE_MAKEFILE ON)
+SET(CMAKE_VERBOSE_MAKEFILE OFF)
 SET(CMAKE_BUILD_TYPE "RelWithDebInfo")
 SET(CMAKE_INCLUDE_CURRENT_DIR ON)
 

libsrc/fort-lib.c

@@ -150,6 +150,7 @@ f2c_maps(int ncid, int varid, const NF_INTEGER* fmaps, ptrdiff_t* cmaps)
     return f2c_strides(ncid, varid, fmaps, cmaps);
 }
 
+#if 0
 #ifdef USE_NETCDF4
 /* These appear to only be defined in netcdf-4*/
 
@@ -274,3 +275,4 @@ nc_inq_compound_field_f(int ncid, nc_type xtype, int fieldid, char *name,
 }
 
 #endif /*USE_NETCDF4*/
+#endif

libsrc/nfconfig.in

@@ -2,6 +2,9 @@
     $Id: nfconfig.in,v 1.11 1997/12/03 17:41:42 steve Exp $ 
 #endif
 
+#undef NF_RELAX_COORD_BOUND
+#undef NF_HAS_PARALLEL4
+#undef NF_HAS_PNETCDF
 
 #ifndef UD_NETCDF_CPP_INC
 #define UD_NETCDF_CPP_INC

libsrc/nfconfig.in.cmake

@@ -2,6 +2,9 @@
     $Id: nfconfig.in,v 1.11 1997/12/03 17:41:42 steve Exp $ 
 #endif
 
+#cmakedefine NF_RELAX_COORD_BOUND 1
+#cmakedefine NF_HAS_PARALLEL4 1
+#cmakedefine NF_HAS_PNETCDF 1
 
 #ifndef UD_NETCDF_CPP_INC
 #define UD_NETCDF_CPP_INC

nf03_test/CMakeLists.txt

@@ -1,4 +1,4 @@
-SET(CMAKE_VERBOSE_MAKEFILE ON)
+SET(CMAKE_VERBOSE_MAKEFILE OFF)
 SET(CMAKE_BUILD_TYPE "RelWithDebInfo")
 SET(CMAKE_INCLUDE_CURRENT_DIR ON)
 

nf03_test/Makefile.am

@@ -117,6 +117,7 @@ if BUILD_V2
 check_PROGRAMS += tst03_f77_v2
 tst03_f77_v2_SOURCES = module_tests.F90 tst03_f77_v2.F handle_err.F
 TESTS += tst03_f77_v2
-CLEANFILES += tst_f77_v2.nc temp.tmp
-
+CLEANFILES += tst_f77_v2.nc
 endif # BUILD_V2
+
+CLEANFILES += temp.tmp