parallel-netcdf: patch for PGI on Cray (#18972)

3 files changed, 69 insertions, 1 deletions

diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/cray_pgi_libtool_master.patch b/var/spack/repos/builtin/packages/parallel-netcdf/cray_pgi_libtool_master.patch
new file mode 100644
index 0000000000..dab9381be6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parallel-netcdf/cray_pgi_libtool_master.patch
@@ -0,0 +1,10 @@
+--- a/m4/libtool.m4
++++ b/m4/libtool.m4
+@@ -5282,7 +5282,6 @@ _LT_EOF
+ 	tmp_sharedflag='-shared'
+ 	case $cc_basename,$host_cpu in
+         pgcc*)				# Portland Group C compiler
+-	  _LT_TAGVAR(whole_archive_flag_spec, $1)='$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'
+ 	  tmp_addflag=' $pic_flag'
+ 	  ;;
+ 	pgf77* | pgf90* | pgf95* | pgfortran*)
diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/cray_pgi_libtool_release.patch b/var/spack/repos/builtin/packages/parallel-netcdf/cray_pgi_libtool_release.patch
new file mode 100644
index 0000000000..dcf34ee962
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parallel-netcdf/cray_pgi_libtool_release.patch
@@ -0,0 +1,26 @@
+--- a/configure
++++ b/configure
+@@ -11858,7 +11858,6 @@ _LT_EOF
+ 	tmp_sharedflag='-shared'
+ 	case $cc_basename,$host_cpu in
+         pgcc*)				# Portland Group C compiler
+-	  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'
+ 	  tmp_addflag=' $pic_flag'
+ 	  ;;
+ 	pgf77* | pgf90* | pgf95* | pgfortran*)
+@@ -21326,7 +21325,6 @@ _LT_EOF
+ 	tmp_sharedflag='-shared'
+ 	case $cc_basename,$host_cpu in
+         pgcc*)				# Portland Group C compiler
+-	  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'
+ 	  tmp_addflag=' $pic_flag'
+ 	  ;;
+ 	pgf77* | pgf90* | pgf95* | pgfortran*)
+@@ -25066,7 +25064,6 @@ _LT_EOF
+ 	tmp_sharedflag='-shared'
+ 	case $cc_basename,$host_cpu in
+         pgcc*)				# Portland Group C compiler
+-	  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'
+ 	  tmp_addflag=' $pic_flag'
+ 	  ;;
+ 	pgf77* | pgf90* | pgf95* | pgfortran*)
diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
index 14c97f6111..8f35ea98c6 100644
--- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py
+++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
@@ -17,6 +17,8 @@ class ParallelNetcdf(AutotoolsPackage):
     url      = "https://parallel-netcdf.github.io/Release/pnetcdf-1.11.0.tar.gz"
     list_url = "https://parallel-netcdf.github.io/wiki/Download.html"
 
+    maintainers = ['skosukhin']
+
     def url_for_version(self, version):
         if version >= Version('1.11.0'):
             url = "https://parallel-netcdf.github.io/Release/pnetcdf-{0}.tar.gz"
@@ -53,12 +55,42 @@ class ParallelNetcdf(AutotoolsPackage):
 
     depends_on('perl', type='build')
 
-    conflicts('+shared', when='@:1.9%nag+fortran')
+    # Suport for shared libraries was introduced in version 1.9.0
     conflicts('+shared', when='@:1.8')
     conflicts('+burstbuffer', when='@:1.10')
 
+    # Before 1.10.0, C utility programs (e.g. ncmpigen) were linked without
+    # explicit specification of the Fortran runtime libraries, which is
+    # required when libpnetcdf.so contains Fortran symbols. Libtool sets the
+    # required linking flags implicitly but only if the Fortran compiler
+    # produces verbose output with the '-v' flag (and, due to a bug in Libtool,
+    # when CXX is not set to 'no'; see macro _LT_LANG_FC_CONFIG in libtool.m4
+    # for more details). The latter is not the case for NAG. Starting 1.10.0,
+    # the required linking flags are explicitly set in the makefiles and
+    # detected using macro AC_FC_LIBRARY_LDFLAGS, which means that we can
+    # override the verbose output flag for Fortran compiler on the command line
+    # (see below).
+    conflicts('+shared', when='@:1.9%nag+fortran')
+
+    # https://github.com/Parallel-NetCDF/PnetCDF/pull/59
     patch('nag_libtool.patch', when='@1.9:1.12.1%nag')
 
+    # We could apply the patch unconditionally. However, it fixes a problem
+    # that manifests itself only when we build shared libraries with Spack on
+    # a Cray system with PGI compiler. Based on the name of the $CC executable,
+    # Libtool "thinks" that it works with PGI compiler directly but on a Cray
+    # system it actually works with the Cray's wrapper. PGI compiler (at least
+    # since the version 15.7) "understands" two formats of the
+    # '--whole-archive' argument. Unluckily, Cray's wrapper "understands" only
+    # one of them but Libtool switches to another one. The following patch
+    # discards the switching.
+    patch('cray_pgi_libtool_release.patch',
+          when='@1.8:999%pgi+shared platform=cray')
+    # Given that the bug manifests itself in rather specific conditions, it is
+    # not reported upstream.
+    patch('cray_pgi_libtool_master.patch',
+          when='@master%pgi+shared platform=cray')
+
     @property
     def libs(self):
         libraries = ['libpnetcdf']