merged changes from master

.travis.yml

@@ -23,8 +23,8 @@ before_script:
   - export CC=mpicc
   - export FC=mpif90
   - export CPPFLAGS='-I/usr/include'
-  - wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz
-  - tar -xzvf pnetcdf-1.12.1.tar.gz
+  - wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz &> /dev/null
+  - tar -xzf pnetcdf-1.12.1.tar.gz
   - pushd pnetcdf-1.12.1
   - ./configure --prefix=/usr --enable-shared --disable-cxx 
   - make
@@ -41,9 +41,9 @@ env:
 script:
   - nc-config --all
   - autoreconf -i
-  - export CFLAGS='-std=c99  -fsanitize=address -fno-omit-frame-pointer -Werror'
-  - export FFLAGS='-fsanitize=address -fno-omit-frame-pointer'
-  - export FCFLAGS='-fsanitize=address -fno-omit-frame-pointer -Werror'
+  - export CFLAGS='-g -std=c99  -fsanitize=address -fno-omit-frame-pointer -Werror'
+  - export FFLAGS='-g -fsanitize=address -fno-omit-frame-pointer'
+  - export FCFLAGS='-g -fsanitize=address -fno-omit-frame-pointer -Werror'
   - export DISTCHECK_CONFIGURE_FLAGS='--enable-fortran'
   - ./configure --enable-fortran --enable-developer-docs
   - make -j distcheck

Makefile.am

@@ -14,5 +14,5 @@ endif
 SUBDIRS = src tests examples ${DOC} scripts cmake
 
 # Add these files to the distribution.
-EXTRA_DIST = CMakeLists.txt set_flags.am COPYRIGHT cmake_config.h.in	\
+EXTRA_DIST = CMakeLists.txt COPYRIGHT cmake_config.h.in	\
 libpio.settings.in

cmake_config.h.in

@@ -5,8 +5,6 @@
  */
 #ifndef _PIO_CONFIG_
 #define _PIO_CONFIG_
-/* Set to avoid warning in intel19 compiler wrt strnlen */
-#define _GNU_SOURCE
 
 /** The major part of the version number. */
 #define PIO_VERSION_MAJOR @VERSION_MAJOR@
@@ -35,4 +33,9 @@
 #cmakedefine HAVE_PAR_FILTERS
 #cmakedefine NETCDF_INTEGRATION
 
+#cmakedefine HAVE_PAR_FILTERS
+#cmakedefine NETCDF_INTEGRATION
+#cmakedefine _NETCDF4
+#cmakedefine _PNETCDF
+
 #endif /* _PIO_CONFIG_ */

configure.ac

@@ -117,6 +117,7 @@ test "x$enable_timing" = xyes || enable_timing=no
 AC_MSG_RESULT([$enable_timing])
 if test "x$enable_timing" = xyes; then
    AC_DEFINE([TIMING], 1, [If true, use GPTL timing library.])
+   AC_DEFINE([HAVE_MPI], [1], [required by GPTL timing library])
 fi
 AM_CONDITIONAL(USE_GPTL, [test "x$enable_timing" = xyes])
 
@@ -224,24 +225,7 @@ if test "x$enable_docs" = xyes; then
    AC_CONFIG_FILES([doc/Doxyfile])
 fi
 
-AC_MSG_NOTICE([setting flags])
-# NetCDF (at least classic) is required for PIO to build.
-AC_DEFINE([_NETCDF], [1], [netCDF classic library available])
-
-# ????
-AC_DEFINE([CPRGNU], [1], [defined by CMake build])
-
-# We must have MPI to build PIO.
-AC_DEFINE([HAVE_MPI], [1], [defined by CMake build])
-
-# ???
-AC_DEFINE([INCLUDE_CMAKE_FCI], [1], [defined by CMake build])
-
-# All builds are on LINUX.
-AC_DEFINE([LINUX], [1], [defined by CMake build])
-
-# Define to solve intel compiler warning.
-AC_DEFINE([_GNU_SOURCE], [1], [solve strnlen declared implicitly warning on intel compiler])
+AC_MSG_NOTICE([finding libraries])
 
 # Check for netCDF library.
 AC_CHECK_LIB([netcdf], [nc_create], [], [AC_MSG_ERROR([Can't find or link to the netcdf library.])])

examples/basic/gdecomp_mod.F90

@@ -300,9 +300,7 @@ end subroutine gdecomp_print
 !==================================================================
    subroutine gdecomp_DOF(gdecomp,my_task,DOF,start,count,write_decomp,test)
 
-#ifdef _NETCDF
    use netcdf   ! _EXTERNAL
-#endif
 
    implicit none
 
@@ -712,7 +710,6 @@ subroutine gdecomp_DOF(gdecomp,my_task,DOF,start,count,write_decomp,test)
 
    ! --- write out arrays ---
 
-#ifdef _NETCDF
    if (wdecomp) then
    write(6,*) ' '
    write(6,*) trim(subname),' writing decomp info to file ',trim(ncname)
@@ -738,7 +735,6 @@ subroutine gdecomp_DOF(gdecomp,my_task,DOF,start,count,write_decomp,test)
    rcode = nf90_put_var(ncid,varid(2),tskid)
    rcode = nf90_close(ncid)
    endif
-#endif
 
    endif   ! testonly
 

examples/basic/testpio.F90

@@ -770,11 +770,7 @@ program testpio
         !   print *, __FILE__,__LINE__,'>',fname_r8,'<'
         !   print *, __FILE__,__LINE__,'>',fname_i4,'<'
         !   print *, __FILE__,__LINE__,'>',fname_r4,'<'
-#if defined(_NETCDF) || defined(_PNETCDF)
         mode = pio_64bit_offset
-#else
-        mode = 0
-#endif
 
         if(writePhase) then 
            if(TestCombo) then

examples/f03/CMakeLists.txt

@@ -15,6 +15,6 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -O0")
 if(${PIO_BUILD_TIMING})
   SET(TIMING_LINK_LIB timing)
 endif()
-SET(SRC examplePio.f90)
+SET(SRC examplePio.F90)
 ADD_EXECUTABLE(examplePio_f90 ${SRC})
 TARGET_LINK_LIBRARIES(examplePio_f90 piof pioc ${TIMING_LINK_LIB})

examples/f03/Makefile.am

@@ -3,8 +3,8 @@
 
 # Ed Hartnett 7/17/19
 
-# Put together AM_CPPFLAGS and AM_LDFLAGS.
-include $(top_srcdir)/set_flags.am
+# Find the pio.mod file.
+AM_CPPFLAGS = -I$(top_srcdir)/src/flib
 
 AM_FCFLAGS = -I$(top_srcdir)/src/flib
 
@@ -14,7 +14,7 @@ ${top_builddir}/src/clib/libpioc.la
 # Build the test for make check.
 check_PROGRAMS = examplePio
 
-examplePio_SOURCES = examplePio.f90
+examplePio_SOURCES = examplePio.F90
 
 if RUN_TESTS
 # Tests will run from a bash script.

examples/f03/examplePio.f90 → examples/f03/examplePio.F90

@@ -1,3 +1,4 @@
+#include "config.h"
 !> @file
 !! A simple Fortran example for the ParallelIO Library.
 module pioExample

libpio.settings.in

@@ -22,7 +22,7 @@ Extra libraries:	@LIBS@
 Fortran Compiler:       @FC_VERSION@
 FFLAGS:                 @FFLAGS@
 FCFLAGS:                @FCFLAGS@
-FPPFLAGS:               @FPPFLAGS@
+More Fortran Flags:	@FPPFLAGS@
 
 # Features
 --------

src/flib/Makefile.am

@@ -7,8 +7,6 @@
 # The library we are building.
 lib_LTLIBRARIES = libpiof.la
 
-AM_CPPFLAGS = -D_NETCDF -D_NETCDF4 -D_PNETCDF
-
 # These linker flags specify libtool version info.
 # See http://www.gnu.org/software/libtool/manual/libtool.html#Libtool-versioning
 # for information regarding incrementing `-version-info`.
@@ -97,15 +95,15 @@ if BUILD_DOCS
 BUILT_SOURCES += piodarray.f90 piolib_mod.f90 pionfatt_mod.f90 pionfget_mod.f90 \
 pionfput_mod.f90 pionfatt_mod_2.f90 pionfget_mod_2.f90
 piodarray.f90: piodarray.F90
-	$(CC) -E $< > $@
+	$(CC) -I../.. $(AM_CPPFLAGS) -E $< > $@
 piolib_mod.f90: piolib_mod.F90
 	$(CC) -I../.. $(AM_CPPFLAGS) -E $< > $@
 pionfatt_mod.f90: pionfatt_mod.F90
-	$(CC) -E $< > $@
+	$(CC) -I../.. $(AM_CPPFLAGS) -E $< > $@
 pionfget_mod.f90: pionfget_mod.F90
-	$(CC) -E $< > $@
+	$(CC) -I../.. $(AM_CPPFLAGS) -E $< > $@
 pionfput_mod.f90: pionfput_mod.F90
-	$(CC) -E $< > $@
+	$(CC) -I../.. $(AM_CPPFLAGS) -E $< > $@
 
 # Unfortunately the genf90.pl script which generates these fortran
 # files has no way of handling doxygen documentation. So use sed to

src/flib/pio.F90

@@ -39,9 +39,7 @@ module pio
        pio_iotype_pnetcdf,pio_iotype_netcdf, &
        pio_global, pio_char, pio_write, pio_nowrite, pio_clobber, pio_noclobber, &
        pio_max_name, pio_max_var_dims, pio_rearr_subset, pio_rearr_box, &
-#if defined(_NETCDF) || defined(_PNETCDF)
        pio_nofill, pio_unlimited, pio_fill_int, pio_fill_double, pio_fill_float, &
-#endif
        pio_64bit_offset, pio_64bit_data, &
        pio_internal_error, pio_bcast_error, pio_return_error, pio_default
 

src/flib/pio_kinds.F90

@@ -4,6 +4,7 @@
 !! types like integer, character, logical, real4 and real8.
 !!
 !<
+#include "config.h"
  module pio_kinds
 
 !  uses mpi if available

src/flib/pio_nf.F90

@@ -1,3 +1,4 @@
+#include "config.h"
 !>
 !! @file
 !! Code to implement the classic netCDF Fortran API in PIO.

src/flib/pio_support.F90

@@ -1,3 +1,4 @@
+#include "config.h"
 !>
 !! @file
 !! Internal code for compiler workarounds, aborts and debug functions.

src/flib/pio_types.F90

@@ -1,3 +1,4 @@
+#include "config.h"
 !>
 !! @file
 !! Derived datatypes and constants for PIO Fortran API.

src/flib/piodarray.F90.in

@@ -1,4 +1,5 @@
 #define __PIO_FILE__ 'piodarray'
+#include "config.h"
 !>
 !! @file
 !! Read and write routines for decomposed data.

src/flib/pionfatt_mod.F90.in

@@ -1,4 +1,5 @@
 #define __PIO_FILE__ "pionfatt_mod.F90"
+#include "config.h"
 !>
 !! @file
 !! @brief NetCDF attribute interface to PIO

src/flib/pionfget_mod.F90.in

@@ -1,4 +1,5 @@
 #define __PIO_FILE__ "pionfget_mod.F90"
+#include "config.h"
 !>
 !! @file
 !! @brief Read Routines for non-decomposed NetCDF data.

src/flib/pionfput_mod.F90.in

@@ -1,4 +1,5 @@
 #define __PIO_FILE__ "pionfput_mod.F90"
+#include "config.h"
 !>
 !! @file
 !! @brief Write routines for non-decomposed NetCDF data.

tests/cunit/test_common.c

@@ -137,10 +137,9 @@ get_iotypes(int *num_flavors, int *flavors)
     num++;
     format[fmtidx++] = PIO_IOTYPE_PNETCDF;
 #endif
-#ifdef _NETCDF
+    /* NetCDF is always present. */
     num++;
     format[fmtidx++] = PIO_IOTYPE_NETCDF;
-#endif
 #ifdef _NETCDF4
     num += 2;
     format[fmtidx++] = PIO_IOTYPE_NETCDF4C;

tests/cunit/test_darray_frame.c

@@ -192,7 +192,7 @@ int main(int argc, char **argv)
 
     /* Initialize test. */
     if ((ret = pio_test_init2(argc, argv, &my_rank, &ntasks, MIN_NTASKS,
-                              MIN_NTASKS, 3, &test_comm)))
+                              MIN_NTASKS, -1, &test_comm)))
         ERR(ERR_INIT);
 
     if ((ret = PIOc_set_iosystem_error_handling(PIO_DEFAULT, PIO_RETURN_ERROR, NULL)))

tests/cunit/test_iosystem3.c

@@ -56,7 +56,7 @@ int create_file(MPI_Comm comm, int iosysid, int format, char *filename,
         return ret;
 
     /* Write an attribute. */
-    if ((ret = PIOc_put_att_text(ncid, varid, attname, strnlen(filename, PIO_TF_MAX_STR_LEN),
+    if ((ret = PIOc_put_att_text(ncid, varid, attname, strlen(filename),
 				 filename)))
         return ret;
 
@@ -94,11 +94,11 @@ int check_file(MPI_Comm comm, int iosysid, int format, int ncid, char *filename,
 
     /* Check the attribute. Null terminating byte deliberately ignored
      * to match fortran code. */
-    if (!(att_data = malloc(strnlen(filename, PIO_TF_MAX_STR_LEN) * sizeof(char))))
+    if (!(att_data = malloc(strlen(filename) * sizeof(char))))
         return PIO_ENOMEM;
     if ((ret = PIOc_get_att(ncid, varid, attname, att_data)))
         return ret;
-    if (strncmp(att_data, filename, strnlen(filename, PIO_TF_MAX_STR_LEN)))
+    if (strncmp(att_data, filename, strlen(filename)))
         return ERR_WRONG;
     free(att_data);
 

tests/fncint/Makefile.am

@@ -3,8 +3,8 @@
 
 # Ed Hartnett 7/3/19
 
-# Put together AM_CPPFLAGS and AM_LDFLAGS.
-include $(top_srcdir)/set_flags.am
+# Find the pio.mod file.
+AM_CPPFLAGS = -I$(top_srcdir)/src/flib
 
 # Link to the PIO Fortran and C libraries.
 LDADD = ${top_builddir}/src/flib/libpiof.la ${top_builddir}/src/clib/libpioc.la

tests/general/Makefile.am

@@ -6,11 +6,11 @@
 # Parallel builds don't currently work in this directory.
 .NOTPARALLEL:
 
-# Put together AM_CPPFLAGS and AM_LDFLAGS.
-include $(top_srcdir)/set_flags.am
+# Find the pio.mod file.
+AM_CPPFLAGS = -I$(top_srcdir)/src/flib
 
-LDADD = libpio_tutil.la	\
-${top_builddir}/src/flib/libpiof.la		\
+# Link to our test, fortran, and C libraries.
+LDADD = libpio_tutil.la ${top_builddir}/src/flib/libpiof.la	\
 ${top_builddir}/src/clib/libpioc.la
 
 # There is a test utility mod file in this subdir which must be built.

tests/general/ncdf_fail.F90.in

@@ -1,3 +1,4 @@
+#include "config.h"
 MODULE ncdf_fail_tgv
   use pio_tutil
   implicit none

tests/general/ncdf_get_put.F90.in

@@ -1,3 +1,4 @@
+#include "config.h"
 PIO_TF_TEMPLATE<PIO_TF_PREDEF_TYPENAME PIO_TF_DATA_TYPE, PIO_TF_PREDEF_TYPENAME PIO_TF_FC_DATA_TYPE>
 PIO_TF_AUTO_TEST_SUB_BEGIN test_put_1datt
   Implicit none

tests/general/ncdf_inq.F90.in

@@ -1,3 +1,4 @@
+#include "config.h"
 MODULE ncdf_inq_tests_tgv
   use pio_tutil
   character(len=PIO_TF_MAX_STR_LEN), parameter :: tgv_fname = "pio_ncdf_inq_test_file.nc"

tests/general/ncdf_simple_tests.F90.in

@@ -1,3 +1,4 @@
+#include "config.h"
 MODULE ncdf_simple_tests_tgv
   use pio_tutil
   ! tgv in prefix corresponds to module name (ncdf_simple_tests_tgv)

tests/general/pio_decomp_fillval.F90.in

@@ -1,3 +1,4 @@
+#include "config.h"
 ! nc write 1d array with fillvalues (the holes are explicitly specified)
 PIO_TF_TEMPLATE<PIO_TF_PREDEF_TYPENAME PIO_TF_DATA_TYPE, PIO_TF_PREDEF_TYPENAME PIO_TF_FC_DATA_TYPE>
 PIO_TF_AUTO_TEST_SUB_BEGIN nc_write_1d_explicit_fval

tests/general/pio_decomp_frame_tests.F90.in

@@ -1,3 +1,4 @@
+#include "config.h"
 ! Get a 3D column decomposition
 ! If force_rearrange is FALSE, the decomposition is such that
 ! # All even procs have VEC_HGT_SZ blocks of 

tests/general/pio_decomp_tests.F90.in

@@ -1,3 +1,4 @@
+#include "config.h"
 PIO_TF_AUTO_TEST_SUB_BEGIN init_decomp_1d_get_loc_sz
   implicit none
   integer, parameter :: VEC_LOCAL_SZ = 7

tests/general/pio_decomp_tests_1d.F90.in

@@ -1,3 +1,4 @@
+#include "config.h"
 ! Get a block cyclic decomposition
 ! If force_rearrange is FALSE, the decomposition is such that
 ! # All even procs have VEC_LOCAL_SZ elements

tests/general/pio_decomp_tests_2d.F90.in

@@ -1,3 +1,4 @@
+#include "config.h"
 ! Get a 2D column decomposition
 ! If force_rearrange is FALSE, the decomposition is such that
 ! # All even procs have VEC_COL_SZ rows of VEC_ROW_SZ elements

tests/general/pio_decomp_tests_3d.F90.in

@@ -1,3 +1,4 @@
+#include "config.h"
 ! Get a 3D column decomposition
 ! If force_rearrange is FALSE, the decomposition is such that
 ! # All even procs have VEC_HGT_SZ blocks of 

tests/general/pio_fail.F90.in

@@ -1,3 +1,4 @@
+#include "config.h"
 PIO_TF_AUTO_TEST_SUB_BEGIN fail_rank_even
   LOGICAL cond
   ! Even procs fail

tests/general/pio_file_fail.F90.in

@@ -1,3 +1,4 @@
+#include "config.h"
 PIO_TF_TEST_SUB_BEGIN create_file_always_fail(iotype, filename)
   implicit none
   integer,  intent(in)  :: iotype