Parallel-netcdf: update package. (#15359)

* Parallel-netcdf: update package.

* Add a temporary patch for version 'develop'.

* Rename version 'develop' to 'master'.

* Drop the patch for 'master'.

2 files changed, 127 insertions, 26 deletions

diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/nag_libtool.patch b/var/spack/repos/builtin/packages/parallel-netcdf/nag_libtool.patch
new file mode 100644
index 0000000000..f391c1dc5e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parallel-netcdf/nag_libtool.patch
@@ -0,0 +1,69 @@
+--- a/configure
++++ b/configure
+@@ -11745,6 +11745,8 @@ _LT_EOF
+ 	  whole_archive_flag_spec=
+ 	  tmp_sharedflag='--shared' ;;
+         nagfor*)                        # NAGFOR 5.3
++          whole_archive_flag_spec='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
++          compiler_needs_object=yes
+           tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+@@ -21030,6 +21032,8 @@ _LT_EOF
+ 	  whole_archive_flag_spec_F77=
+ 	  tmp_sharedflag='--shared' ;;
+         nagfor*)                        # NAGFOR 5.3
++          whole_archive_flag_spec_F77='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
++          compiler_needs_object_F77=yes
+           tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+@@ -24765,6 +24769,8 @@ _LT_EOF
+ 	  whole_archive_flag_spec_FC=
+ 	  tmp_sharedflag='--shared' ;;
+         nagfor*)                        # NAGFOR 5.3
++          whole_archive_flag_spec_FC='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
++          compiler_needs_object_FC=yes
+           tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+--- a/scripts/ltmain.sh
++++ b/scripts/ltmain.sh
+@@ -7862,6 +7862,13 @@ func_mode_link ()
+ 	# Convert "-framework foo" to "foo.ltframework"
+ 	if test -n "$inherited_linker_flags"; then
+ 	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
++
++	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
++	  func_cc_basename $CC
++	  case $func_cc_basename_result in
++	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
++	  esac
++
+ 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
+ 	    case " $new_inherited_linker_flags " in
+ 	      *" $tmp_inherited_linker_flag "*) ;;
+@@ -8881,7 +8888,8 @@ func_mode_link ()
+ 	  xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
+ 	  verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
+           # On Darwin other compilers
+-          case $CC in
++          func_cc_basename $CC
++          case $func_cc_basename_result in
+               nagfor*)
+                   verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
+                   ;;
+@@ -9493,6 +9501,13 @@ EOF
+ 	  ;;
+       esac
+ 
++      # Time to revert the changes made for nagfor.
++      func_cc_basename $CC
++      case $func_cc_basename_result in
++        nagfor*)
++          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
++      esac
++
+       # move library search paths that coincide with paths to not yet
+       # installed libraries to the beginning of the library search list
+       new_libs=
diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
index 34a1af5984..384717d05e 100644
--- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py
+++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
@@ -25,7 +25,6 @@ class ParallelNetcdf(AutotoolsPackage):
 
         return url.format(version.dotted)
 
-    version('develop', branch='develop')
     version('master', branch='master')
     version('1.12.1', sha256='56f5afaa0ddc256791c405719b6436a83b92dcd5be37fe860dea103aee8250a2')
     version('1.11.2', sha256='d2c18601b364c35b5acb0a0b46cd6e14cae456e0eb854e5c789cf65f3cd6a2a7')
@@ -42,41 +41,74 @@ class ParallelNetcdf(AutotoolsPackage):
     variant('fortran', default=True, description='Build the Fortran Interface')
     variant('pic', default=True,
             description='Produce position-independent code (for shared libs)')
+    variant('shared', default=True, description='Enable shared library')
 
     depends_on('mpi')
 
     depends_on('m4', type='build')
+    depends_on('autoconf', when='@master', type='build')
+    depends_on('automake', when='@master', type='build')
+    depends_on('libtool', when='@master', type='build')
 
-    # See:
-    # https://trac.mcs.anl.gov/projects/parallel-netcdf/browser/trunk/INSTALL
-    def configure_args(self):
-        spec = self.spec
+    conflicts('+shared', when='@:1.9%nag+fortran')
+    conflicts('+shared', when='@:1.8')
+
+    patch('nag_libtool.patch', when='@1.9:1.12.1%nag')
 
-        args = ['--with-mpi={0}'.format(spec['mpi'].prefix)]
-        args.append('MPICC={0}'.format(spec['mpi'].mpicc))
-        args.append('MPICXX={0}'.format(spec['mpi'].mpicxx))
-        args.append('MPIF77={0}'.format(spec['mpi'].mpifc))
-        args.append('MPIF90={0}'.format(spec['mpi'].mpifc))
-        args.append('SEQ_CC={0}'.format(spack_cc))
+    @property
+    def libs(self):
+        libraries = ['libpnetcdf']
 
-        if '+pic' in spec:
-            args.extend([
-                'CFLAGS={0}'.format(self.compiler.pic_flag),
-                'CXXFLAGS={0}'.format(self.compiler.pic_flag),
-                'FFLAGS={0}'.format(self.compiler.pic_flag)
-            ])
+        query_parameters = self.spec.last_query.extra_parameters
+
+        if 'shared' in query_parameters:
+            shared = True
+        elif 'static' in query_parameters:
+            shared = False
+        else:
+            shared = '+shared' in self.spec
 
-        if '~cxx' in spec:
-            args.append('--disable-cxx')
+        libs = find_libraries(
+            libraries, root=self.prefix, shared=shared, recursive=True
+        )
 
-        if '~fortran' in spec:
-            args.append('--disable-fortran')
+        if libs:
+            return libs
 
-        if spec.satisfies('@1.8.0:'):
+        msg = 'Unable to recursively locate {0} {1} libraries in {2}'
+        raise spack.error.NoLibrariesError(
+            msg.format('shared' if shared else 'static',
+                       self.spec.name,
+                       self.spec.prefix))
+
+    @when('@master')
+    def autoreconf(self, spec, prefix):
+        with working_dir(self.configure_directory):
+            # We do not specify '-f' because we need to use libtool files from
+            # the repository.
+            autoreconf('-iv')
+
+    def configure_args(self):
+        args = ['--with-mpi=%s' % self.spec['mpi'].prefix,
+                'SEQ_CC=%s' % spack_cc]
+
+        args += self.enable_or_disable('cxx')
+        args += self.enable_or_disable('fortran')
+
+        if '+pic' in self.spec:
+            args.extend(['{0}FLAGS={1}'.format(lang, self.compiler.pic_flag)
+                         for lang in ['C', 'CXX', 'F', 'FC']])
+
+        if self.version >= Version('1.8'):
             args.append('--enable-relax-coord-bound')
 
-        return args
+        if self.version >= Version('1.9'):
+            args += self.enable_or_disable('shared')
+            args.extend(['--enable-static',
+                         '--disable-silent-rules'])
+
+        if self.spec.satisfies('%nag+fortran+shared'):
+            args.extend(['ac_cv_prog_fc_v=-Wl,-v',
+                         'ac_cv_prog_f77_v=-Wl,-v'])
 
-    def install(self, spec, prefix):
-        # Installation fails in parallel
-        make('install', parallel=False)
+        return args