add patch from Sergey Kosukhin to make sure that we do not have unresolved MPI symbols in libsct.so

autogen.sh

@@ -12,12 +12,28 @@ verlte $libtool_version 2.4.2 && {
   # fix m4/libtool.m4 for nagfor sharedflag
   # see https://trac.mpich.org/projects/mpich/ticket/1870 for details
   patch --forward --no-backup-if-mismatch -p0 -s -l < maint/libtool.m4.patch
+}
 
-  # rebuild configure
-  autoconf -f || exit $?
+# Fix the problem when creating shared library with libtool and using MPI
+# compiler wrapper. When LT_INIT is called before AX_PROG_FC_MPI in the
+# configure.ac, the generated ./libtool doesn't know about the MPI
+# compiler wrapper, which we do need since the logic of the script
+# depends on the name of the compiler executable name (e.g. nagfor).
+# But we also want to be able to link shared libraries using MPIFC.
+# AX_PROG_FC_MPI sets FC=$MPIFC but ./libtool keeps using the hardcoded
+# command that uses the actual compiler when creating a shared library.
+# This patch instructs ./libtool to check whether $FC is set. If $FC
+# is set ./libtool will use it for linking, and will act as usual otherwise.
+# See also https://lists.gnu.org/archive/html/libtool/2012-05/msg00002.html
+patch --forward --no-backup-if-mismatch -p0 -s -l < maint/libtool.m4.hardcoded.patch
 
-  # Reset libtool.m4 timestamps to avoid confusing make 
-  touch -r m4/ltversion.m4 m4/libtool.m4
-}
+# rebuild configure
+autoconf -f || exit $?
 
+# Reset libtool.m4 timestamps to avoid confusing make 
+touch -r m4/ltversion.m4 m4/libtool.m4
+
+# Libtool duplicates some of the command line flags (e.g. -fopenmp)
+# when calling the actual compiler. nagfor considers this as an error.
 patch --forward --no-backup-if-mismatch -p0 -s -l < maint/ltmain.sh.patch
+

configure.ac

@@ -19,6 +19,8 @@ AM_INIT_AUTOMAKE([1.14 silent-rules no-dependencies])
 AM_EXTRA_RECURSIVE_TARGETS([doc])
 AC_CONFIG_SRCDIR([src/sct_reporter.c])
 
+dnl LT_INIT must be called before AX_PROG_FC_MPI, otherwise
+dnl it won't find out how to work with the underlying compiler.
 LT_INIT([pic-only])
 
 #

m4/ax_prog_fc_mpi.m4

@@ -16,8 +16,7 @@
 #
 #   MPI-WANTED-TEST is used to test whether MPI is actually wanted by the
 #   user. If MPI-WANTED_TEST is omitted or if it succeeds, the macro will
-#   try to find out how to use MPI, if it fails, the macro will call
-#   AC_PROG_CC to find a standard C compiler instead.
+#   try to find out how to use MPI.
 #
 #   When MPI is found, ACTION-IF-FOUND will be executed, if MPI is not found
 #   (or MPI-WANTED-TEST fails) ACTION-IF-NOT-FOUND is executed. If
@@ -80,6 +79,7 @@ AC_PREREQ(2.50)
 # Check for compiler
 # Needs to be split off into an extra macro to ensure right expansion
 # order.
+AC_REQUIRE([AC_PROG_FC])
 AC_REQUIRE([_AX_PROG_FC_MPI],[_AX_PROG_FC_MPI([$1])])
 
 AS_IF([test x"$_ax_prog_fc_mpi_mpi_wanted" = xno],
@@ -161,8 +161,11 @@ AC_DEFUN_ONCE([_AX_PROG_FC_MPI], [
       AC_MSG_WARN([using FC=$FC as MPIFC compiler.])
       MPIFC="$FC"
     elif test -n "$FC" && test -n "$MPIFC"; then
-      AC_MSG_WARN([overwriting FC=$MPIFC.])
-      FC="$MPIFC"
+      dnl extract found options from FC if overriden by MPIFC
+      fc_opts="$FC "
+      fc_opts=${fc_opts#* }
+      AC_MSG_WARN([overwriting FC='$MPIFC $fc_opts'. was FC='$FC' ; MPIFC='$MPIFC'])
+      FC="$MPIFC $fc_opts"
     fi
   fi
 

maint/libtool.m4.hardcoded.patch

+--- m4/libtool.m4	2018-07-19 16:29:39.928156909 +0200
++++ m4/libtool.m4.hardcoded.patched	2018-07-19 16:26:58.730540710 +0200
+@@ -6048,6 +6048,9 @@
+       esac
+     fi
+   fi
++  m4_ifval([$1],
++    [_LT_TAGVAR(archive_cmds, $1)=`AS_ECHO(["$_LT_TAGVAR(archive_cmds, $1)"]) | sed 's%\(\\\\\)\?\$CC%\\${FC:-\1$CC}%g'`
++    _LT_TAGVAR(archive_expsym_cmds, $1)=`AS_ECHO(["$_LT_TAGVAR(archive_expsym_cmds, $1)"]) | sed 's%\(\\\\\)\?\$CC%\\${FC:-\1$CC}%g'`])
+ ])
+ AC_MSG_RESULT([$_LT_TAGVAR(ld_shlibs, $1)])
+ test no = "$_LT_TAGVAR(ld_shlibs, $1)" && can_build_shared=no

src/Makefile.am

@@ -4,7 +4,7 @@ AM_FCFLAGS = $(FC_MODINC).. $(FCFLAGS_f90) $(FCDEFS)
 lib_LTLIBRARIES = libsct.la
 libsct_la_LIBADD = $(LTLIBPAPI) $(LTLIBHDF5)
 
-libsct_la_LDFLAGS = $(OPENMP_FC_C_LT_FLAGS) -version-info @LIB_CURRENT@:@LIB_REVISION@:@LIB_AGE@
+libsct_la_LDFLAGS = -Wl,-no-undefined $(OPENMP_FC_C_LT_FLAGS) -version-info @LIB_CURRENT@:@LIB_REVISION@:@LIB_AGE@
 header = $(srcdir)/sct_config.h \
 	$(srcdir)/sct_mach.h \
 	$(srcdir)/sct_collector.h \

tests/.gitignore

@@ -9,4 +9,4 @@ test_serial
 test_omp
 test_mpi
 test_hybrid
-
+test_hdf5_fortran