From 6213867abc475bbc20d61d772d15c1a817edbc82 Mon Sep 17 00:00:00 2001
From: Edward Hartnett <Edward.Hartnett@noaa.gov>
Date: Tue, 18 Aug 2020 06:33:08 -0600
Subject: [PATCH 01/10] cleanup of flag use in src/flib

---
 src/flib/Makefile.am         | 2 --
 src/flib/pio_kinds.F90       | 1 +
 src/flib/pio_nf.F90          | 1 +
 src/flib/pio_support.F90     | 1 +
 src/flib/pio_types.F90       | 1 +
 src/flib/piodarray.F90.in    | 1 +
 src/flib/pionfatt_mod.F90.in | 1 +
 src/flib/pionfget_mod.F90.in | 1 +
 src/flib/pionfput_mod.F90.in | 1 +
 9 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/flib/Makefile.am b/src/flib/Makefile.am
index abb541fdde7..da5bb7331d0 100644
--- a/src/flib/Makefile.am
+++ b/src/flib/Makefile.am
@@ -7,8 +7,6 @@
 # The library we are building.
 lib_LTLIBRARIES = libpiof.la
 
-AM_CPPFLAGS = -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`.
diff --git a/src/flib/pio_kinds.F90 b/src/flib/pio_kinds.F90
index c5074c1f850..f9de9a185aa 100644
--- a/src/flib/pio_kinds.F90
+++ b/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
diff --git a/src/flib/pio_nf.F90 b/src/flib/pio_nf.F90
index b40b7b71356..a8352b294b2 100644
--- a/src/flib/pio_nf.F90
+++ b/src/flib/pio_nf.F90
@@ -1,3 +1,4 @@
+#include "config.h"
 !>
 !! @file
 !! Code to implement the classic netCDF Fortran API in PIO.
diff --git a/src/flib/pio_support.F90 b/src/flib/pio_support.F90
index ae212d1bbdc..686da26fed2 100644
--- a/src/flib/pio_support.F90
+++ b/src/flib/pio_support.F90
@@ -1,3 +1,4 @@
+#include "config.h"
 !>
 !! @file
 !! Internal code for compiler workarounds, aborts and debug functions.
diff --git a/src/flib/pio_types.F90 b/src/flib/pio_types.F90
index 970c2c83402..844514f6171 100644
--- a/src/flib/pio_types.F90
+++ b/src/flib/pio_types.F90
@@ -1,3 +1,4 @@
+#include "config.h"
 !>
 !! @file
 !! Derived datatypes and constants for PIO Fortran API.
diff --git a/src/flib/piodarray.F90.in b/src/flib/piodarray.F90.in
index dfd2b5339a2..e9b5252a5ed 100644
--- a/src/flib/piodarray.F90.in
+++ b/src/flib/piodarray.F90.in
@@ -1,4 +1,5 @@
 #define __PIO_FILE__ 'piodarray'
+#include "config.h"
 !>
 !! @file
 !! Read and write routines for decomposed data.
diff --git a/src/flib/pionfatt_mod.F90.in b/src/flib/pionfatt_mod.F90.in
index cc4a3cd409d..da4e91d7c59 100644
--- a/src/flib/pionfatt_mod.F90.in
+++ b/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
diff --git a/src/flib/pionfget_mod.F90.in b/src/flib/pionfget_mod.F90.in
index 3fe5462d95a..fd98155e9b5 100644
--- a/src/flib/pionfget_mod.F90.in
+++ b/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.
diff --git a/src/flib/pionfput_mod.F90.in b/src/flib/pionfput_mod.F90.in
index 727c7d0dbcd..33024fd963e 100644
--- a/src/flib/pionfput_mod.F90.in
+++ b/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.

From 0a10f86bc1a748ccaa3b28c2faf2162b901ca44e Mon Sep 17 00:00:00 2001
From: Edward Hartnett <Edward.Hartnett@noaa.gov>
Date: Tue, 18 Aug 2020 06:37:10 -0600
Subject: [PATCH 02/10] adding some cmakedefines

---
 cmake_config.h.in | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/cmake_config.h.in b/cmake_config.h.in
index f8917ba563f..65ccd1d4587 100644
--- a/cmake_config.h.in
+++ b/cmake_config.h.in
@@ -32,4 +32,9 @@
 
 #define HAVE_PAR_FILTERS @HAVE_PAR_FILTERS@
 
+#cmakedefine HAVE_PAR_FILTERS
+#cmakedefine NETCDF_INTEGRATION
+#cmakedefine _NETCDF4
+#cmakedefine _PNETCDF
+
 #endif /* _PIO_CONFIG_ */

From db93ea51b2797f2d1b5576947235bf42e4d37122 Mon Sep 17 00:00:00 2001
From: Edward Hartnett <Edward.Hartnett@noaa.gov>
Date: Tue, 18 Aug 2020 06:45:31 -0600
Subject: [PATCH 03/10] more changes so that all fortran files use config.h

---
 src/flib/Makefile.am                        | 8 ++++----
 tests/general/ncdf_fail.F90.in              | 1 +
 tests/general/ncdf_get_put.F90.in           | 1 +
 tests/general/ncdf_inq.F90.in               | 1 +
 tests/general/ncdf_simple_tests.F90.in      | 1 +
 tests/general/pio_decomp_fillval.F90.in     | 1 +
 tests/general/pio_decomp_frame_tests.F90.in | 1 +
 tests/general/pio_decomp_tests.F90.in       | 1 +
 tests/general/pio_decomp_tests_1d.F90.in    | 1 +
 tests/general/pio_decomp_tests_2d.F90.in    | 1 +
 tests/general/pio_decomp_tests_3d.F90.in    | 1 +
 tests/general/pio_fail.F90.in               | 1 +
 tests/general/pio_file_fail.F90.in          | 1 +
 tests/general/pio_file_simple_tests.F90.in  | 1 +
 tests/general/pio_init_finalize.F90.in      | 1 +
 tests/general/pio_iosystem_tests.F90.in     | 1 +
 tests/general/pio_iosystem_tests2.F90.in    | 1 +
 tests/general/pio_iosystem_tests3.F90.in    | 1 +
 tests/general/pio_rearr.F90.in              | 1 +
 tests/general/pio_rearr_opts.F90.in         | 1 +
 tests/general/pio_rearr_opts2.F90.in        | 1 +
 21 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/src/flib/Makefile.am b/src/flib/Makefile.am
index da5bb7331d0..758b1aba8cc 100644
--- a/src/flib/Makefile.am
+++ b/src/flib/Makefile.am
@@ -95,15 +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
diff --git a/tests/general/ncdf_fail.F90.in b/tests/general/ncdf_fail.F90.in
index dfc09148a49..eed98aad6fa 100644
--- a/tests/general/ncdf_fail.F90.in
+++ b/tests/general/ncdf_fail.F90.in
@@ -1,3 +1,4 @@
+#include "config.h"
 MODULE ncdf_fail_tgv
   use pio_tutil
   implicit none
diff --git a/tests/general/ncdf_get_put.F90.in b/tests/general/ncdf_get_put.F90.in
index 7453fe32ede..2d00474cd00 100644
--- a/tests/general/ncdf_get_put.F90.in
+++ b/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
diff --git a/tests/general/ncdf_inq.F90.in b/tests/general/ncdf_inq.F90.in
index 51586d7df27..9745bd1b8e2 100644
--- a/tests/general/ncdf_inq.F90.in
+++ b/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"
diff --git a/tests/general/ncdf_simple_tests.F90.in b/tests/general/ncdf_simple_tests.F90.in
index 272997d0a1c..12368f13000 100644
--- a/tests/general/ncdf_simple_tests.F90.in
+++ b/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)
diff --git a/tests/general/pio_decomp_fillval.F90.in b/tests/general/pio_decomp_fillval.F90.in
index 432adbfbfe3..1b67382e669 100644
--- a/tests/general/pio_decomp_fillval.F90.in
+++ b/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
diff --git a/tests/general/pio_decomp_frame_tests.F90.in b/tests/general/pio_decomp_frame_tests.F90.in
index 791d748052b..70edaf6fbbd 100644
--- a/tests/general/pio_decomp_frame_tests.F90.in
+++ b/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 
diff --git a/tests/general/pio_decomp_tests.F90.in b/tests/general/pio_decomp_tests.F90.in
index b6d7f06d0a4..cb6f9398691 100644
--- a/tests/general/pio_decomp_tests.F90.in
+++ b/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
diff --git a/tests/general/pio_decomp_tests_1d.F90.in b/tests/general/pio_decomp_tests_1d.F90.in
index 866be4c4a8f..52acc3eb4c9 100644
--- a/tests/general/pio_decomp_tests_1d.F90.in
+++ b/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
diff --git a/tests/general/pio_decomp_tests_2d.F90.in b/tests/general/pio_decomp_tests_2d.F90.in
index 5cd711294f7..25b2a488432 100644
--- a/tests/general/pio_decomp_tests_2d.F90.in
+++ b/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
diff --git a/tests/general/pio_decomp_tests_3d.F90.in b/tests/general/pio_decomp_tests_3d.F90.in
index 79569dbaa4e..17a20b2d0e7 100644
--- a/tests/general/pio_decomp_tests_3d.F90.in
+++ b/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 
diff --git a/tests/general/pio_fail.F90.in b/tests/general/pio_fail.F90.in
index 464fc5c5d2a..796670bd87f 100644
--- a/tests/general/pio_fail.F90.in
+++ b/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
diff --git a/tests/general/pio_file_fail.F90.in b/tests/general/pio_file_fail.F90.in
index a4b99acb43c..8ef10631809 100644
--- a/tests/general/pio_file_fail.F90.in
+++ b/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
diff --git a/tests/general/pio_file_simple_tests.F90.in b/tests/general/pio_file_simple_tests.F90.in
index af5604b1798..9fc177ec42a 100644
--- a/tests/general/pio_file_simple_tests.F90.in
+++ b/tests/general/pio_file_simple_tests.F90.in
@@ -1,3 +1,4 @@
+#include "config.h"
 PIO_TF_TEST_SUB_BEGIN create_file_no_opts(iotype, filename)
   implicit none
   integer,  intent(in)  :: iotype
diff --git a/tests/general/pio_init_finalize.F90.in b/tests/general/pio_init_finalize.F90.in
index ab36f00b6f2..27e03f8ea76 100644
--- a/tests/general/pio_init_finalize.F90.in
+++ b/tests/general/pio_init_finalize.F90.in
@@ -1,3 +1,4 @@
+#include "config.h"
 PIO_TF_AUTO_TEST_SUB_BEGIN init_finalize
   ! The default test driver should initialize and finalize PIO
   PRINT *, "Hello world"
diff --git a/tests/general/pio_iosystem_tests.F90.in b/tests/general/pio_iosystem_tests.F90.in
index c5610c5b0ad..2bbf399ec16 100644
--- a/tests/general/pio_iosystem_tests.F90.in
+++ b/tests/general/pio_iosystem_tests.F90.in
@@ -1,3 +1,4 @@
+#include "config.h"
 ! Split comm world into two comms (one with even procs and the other
 ! with odd procs
 SUBROUTINE split_world_odd_even(new_comm, new_rank, new_size, is_even)
diff --git a/tests/general/pio_iosystem_tests2.F90.in b/tests/general/pio_iosystem_tests2.F90.in
index 50a900b4a3d..6d900b73336 100644
--- a/tests/general/pio_iosystem_tests2.F90.in
+++ b/tests/general/pio_iosystem_tests2.F90.in
@@ -1,3 +1,4 @@
+#include "config.h"
 ! Split comm world into two comms (one with even procs and the other
 ! with odd procs
 SUBROUTINE split_world_odd_even(new_comm, new_rank, new_size, is_even)
diff --git a/tests/general/pio_iosystem_tests3.F90.in b/tests/general/pio_iosystem_tests3.F90.in
index fad87a4beb5..6477e05b067 100644
--- a/tests/general/pio_iosystem_tests3.F90.in
+++ b/tests/general/pio_iosystem_tests3.F90.in
@@ -1,3 +1,4 @@
+#include "config.h"
 ! Split comm world into two comms (even procs and odd procs) and
 ! rank == overlapped_rank included in both comms
 SUBROUTINE split_world_two_with_overlap(new_comms, new_ranks, new_sizes, overlapped_rank)
diff --git a/tests/general/pio_rearr.F90.in b/tests/general/pio_rearr.F90.in
index 1cddf87707a..202ad109585 100644
--- a/tests/general/pio_rearr.F90.in
+++ b/tests/general/pio_rearr.F90.in
@@ -1,3 +1,4 @@
+#include "config.h"
 ! Create a file with a global attribute (filename)
 SUBROUTINE create_file(comm, iosys, iotype, fname, attname, dimname, ret)
     use pio_tutil
diff --git a/tests/general/pio_rearr_opts.F90.in b/tests/general/pio_rearr_opts.F90.in
index a47695cb752..d209860c2f7 100644
--- a/tests/general/pio_rearr_opts.F90.in
+++ b/tests/general/pio_rearr_opts.F90.in
@@ -1,3 +1,4 @@
+#include "config.h"
 MODULE pio_rearr_opts_tgv
   use pio_tutil
   character(len=PIO_TF_MAX_STR_LEN), parameter ::tgv_fname ="pio_rearr_opts_test.nc"
diff --git a/tests/general/pio_rearr_opts2.F90.in b/tests/general/pio_rearr_opts2.F90.in
index a46565b5e59..0d6a48c8a83 100644
--- a/tests/general/pio_rearr_opts2.F90.in
+++ b/tests/general/pio_rearr_opts2.F90.in
@@ -1,3 +1,4 @@
+#include "config.h"
 MODULE pio_rearr_opts_tgv
   use pio_tutil
   character(len=PIO_TF_MAX_STR_LEN), parameter ::tgv_fname ="pio_rearr_opts2_test.nc"

From a91eed922aa3f8563b96e86e8fac23b7fc744ed1 Mon Sep 17 00:00:00 2001
From: Edward Hartnett <Edward.Hartnett@noaa.gov>
Date: Tue, 18 Aug 2020 07:27:42 -0600
Subject: [PATCH 04/10] more flag cleanup

---
 tests/general/Makefile.am | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/tests/general/Makefile.am b/tests/general/Makefile.am
index 68ece2cd2fd..38983137b49 100644
--- a/tests/general/Makefile.am
+++ b/tests/general/Makefile.am
@@ -7,10 +7,12 @@
 .NOTPARALLEL:
 
 # Put together AM_CPPFLAGS and AM_LDFLAGS.
-include $(top_srcdir)/set_flags.am
+#include $(top_srcdir)/set_flags.am
 
-LDADD = libpio_tutil.la	\
-${top_builddir}/src/flib/libpiof.la		\
+AM_CPPFLAGS = -I$(top_srcdir)/src/flib -D_NETCDF
+
+# 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.

From 4d6e4f8646a2e8de72636f5b434272d4a7dc268b Mon Sep 17 00:00:00 2001
From: Edward Hartnett <Edward.Hartnett@noaa.gov>
Date: Tue, 18 Aug 2020 07:30:26 -0600
Subject: [PATCH 05/10] more flag cleanup

---
 tests/general/Makefile.am | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tests/general/Makefile.am b/tests/general/Makefile.am
index 38983137b49..35779ca5b7a 100644
--- a/tests/general/Makefile.am
+++ b/tests/general/Makefile.am
@@ -6,10 +6,8 @@
 # Parallel builds don't currently work in this directory.
 .NOTPARALLEL:
 
-# Put together AM_CPPFLAGS and AM_LDFLAGS.
-#include $(top_srcdir)/set_flags.am
-
-AM_CPPFLAGS = -I$(top_srcdir)/src/flib -D_NETCDF
+# Find the pio.mod file.
+AM_CPPFLAGS = -I$(top_srcdir)/src/flib
 
 # Link to our test, fortran, and C libraries.
 LDADD = libpio_tutil.la ${top_builddir}/src/flib/libpiof.la	\

From 7067c6331082b63af3774531fbd7af13edb9fd60 Mon Sep 17 00:00:00 2001
From: Edward Hartnett <Edward.Hartnett@noaa.gov>
Date: Tue, 18 Aug 2020 07:42:17 -0600
Subject: [PATCH 06/10] cleanup of flags in test/unit autotools build

---
 tests/unit/Makefile.am | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/unit/Makefile.am b/tests/unit/Makefile.am
index 33264e29011..1eaea6e77b3 100644
--- a/tests/unit/Makefile.am
+++ b/tests/unit/Makefile.am
@@ -6,8 +6,8 @@
 # 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
 
 # Build the test for make check.
 check_PROGRAMS = pio_unit_test_driver

From 5f190e84e8ae7f10469376904bf359cb5f964447 Mon Sep 17 00:00:00 2001
From: Edward Hartnett <Edward.Hartnett@noaa.gov>
Date: Tue, 18 Aug 2020 08:48:54 -0600
Subject: [PATCH 07/10] more fortran flag cleanup

---
 tests/fncint/Makefile.am             | 4 ++--
 tests/performance/Makefile.am        | 4 ++--
 tests/performance/pioperformance.F90 | 1 +
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/tests/fncint/Makefile.am b/tests/fncint/Makefile.am
index f45c1ca5810..086b11ebaf7 100644
--- a/tests/fncint/Makefile.am
+++ b/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
diff --git a/tests/performance/Makefile.am b/tests/performance/Makefile.am
index 751b970be92..d63c58c4b9d 100644
--- a/tests/performance/Makefile.am
+++ b/tests/performance/Makefile.am
@@ -6,8 +6,8 @@
 # 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
 
 # Link to test util library and PIO Fortran and C libs.
 LDADD = $(top_builddir)/src/gptl/libperf_mod.la	\
diff --git a/tests/performance/pioperformance.F90 b/tests/performance/pioperformance.F90
index cb293158740..8a5e2e732b0 100644
--- a/tests/performance/pioperformance.F90
+++ b/tests/performance/pioperformance.F90
@@ -1,3 +1,4 @@
+#include "config.h"
 #define VARINT 1
 !#define VARREAL 1
 !#define VARDOUBLE 1

From 5b7f801042774f4c2ec42c397acf29da707cd00d Mon Sep 17 00:00:00 2001
From: Edward Hartnett <Edward.Hartnett@noaa.gov>
Date: Tue, 18 Aug 2020 08:56:31 -0600
Subject: [PATCH 08/10] more fortran flag cleanup

---
 Makefile.am                 |  2 +-
 examples/f03/Makefile.am    |  4 ++--
 examples/f03/examplePio.f90 |  1 +
 set_flags.am                | 18 ------------------
 4 files changed, 4 insertions(+), 21 deletions(-)
 delete mode 100644 set_flags.am

diff --git a/Makefile.am b/Makefile.am
index faa7feb3f4e..8d6fc16db28 100644
--- a/Makefile.am
+++ b/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
diff --git a/examples/f03/Makefile.am b/examples/f03/Makefile.am
index 9a8781d20ad..fc885d0878d 100644
--- a/examples/f03/Makefile.am
+++ b/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
 
diff --git a/examples/f03/examplePio.f90 b/examples/f03/examplePio.f90
index d2baddf2096..88804b7acab 100644
--- a/examples/f03/examplePio.f90
+++ b/examples/f03/examplePio.f90
@@ -1,3 +1,4 @@
+#include "config.h"
 !> @file
 !! A simple Fortran example for the ParallelIO Library.
 module pioExample
diff --git a/set_flags.am b/set_flags.am
deleted file mode 100644
index 08efa30db22..00000000000
--- a/set_flags.am
+++ /dev/null
@@ -1,18 +0,0 @@
-# This is part of the PIO package.
-#
-# Assemble the CPPFLAGS and for PIO Fortran tests.
-#
-# Ed Hartnett 3/26/19
-
-# Set the CPPFLAGS.
-AM_CPPFLAGS = -I$(top_srcdir)/src/flib -D_NETCDF
-
-# Is the user building with pnetcdf?
-if BUILD_PNETCDF
-AM_CPPFLAGS += -D_PNETCDF
-endif
-
-# Is the user building with netCDF-4 parallel I/O?
-if BUILD_NETCDF4
-AM_CPPFLAGS += -D_NETCDF4
-endif

From 089a7ecc634ab757dcdba3d725dfe4fc321cda23 Mon Sep 17 00:00:00 2001
From: Edward Hartnett <Edward.Hartnett@noaa.gov>
Date: Tue, 18 Aug 2020 09:12:41 -0600
Subject: [PATCH 09/10] turning off logging in a test

---
 tests/cunit/test_darray_frame.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/cunit/test_darray_frame.c b/tests/cunit/test_darray_frame.c
index 949e90ebfb4..41f43452360 100644
--- a/tests/cunit/test_darray_frame.c
+++ b/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)))

From a1a04ef2e8cb03f25d0b59c372d2985c5ccc7186 Mon Sep 17 00:00:00 2001
From: Edward Hartnett <Edward.Hartnett@noaa.gov>
Date: Tue, 18 Aug 2020 09:16:13 -0600
Subject: [PATCH 10/10] moved .f90 to .F90

---
 examples/f03/CMakeLists.txt                     | 2 +-
 examples/f03/Makefile.am                        | 2 +-
 examples/f03/{examplePio.f90 => examplePio.F90} | 0
 3 files changed, 2 insertions(+), 2 deletions(-)
 rename examples/f03/{examplePio.f90 => examplePio.F90} (100%)

diff --git a/examples/f03/CMakeLists.txt b/examples/f03/CMakeLists.txt
index a299c7cde8c..1073fda1a94 100644
--- a/examples/f03/CMakeLists.txt
+++ b/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})
diff --git a/examples/f03/Makefile.am b/examples/f03/Makefile.am
index fc885d0878d..6f995163fda 100644
--- a/examples/f03/Makefile.am
+++ b/examples/f03/Makefile.am
@@ -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.
diff --git a/examples/f03/examplePio.f90 b/examples/f03/examplePio.F90
similarity index 100%
rename from examples/f03/examplePio.f90
rename to examples/f03/examplePio.F90