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Update flag_handler for 'netcdf-fortran'. (#14789)

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* Update flag_handler for 'netcdf-fortran'.

* Refactoring.

* Enable old versions of netcdf-fortran for NAG.

* Disable parallel 'make check' for versions before 4.5.0.

* Fix shared libraries built with NAG instead of conflicting it.

* Add 'skosukhin' as a maintainer of 'netcdf-fortran'.
This commit is contained in:
Sergey Kosukhin 2020-03-02 15:40:37 +01:00 committed by GitHub
parent aae59f4866
commit e3b357ad87
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
7 changed files with 612 additions and 42 deletions
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312
var/spack/repos/builtin/packages/netcdf-fortran/excessive_linking.patch Normal file
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@ -0,0 +1,312 @@
--- a/config.h.in
+++ b/config.h.in
@@ -52,9 +52,6 @@
/* Define to 1 if you have the <inttypes.h> header file. */
#undef HAVE_INTTYPES_H
-/* Define to 1 if you have the `curl' library (-lcurl). */
-#undef HAVE_LIBCURL
-
/* Define to 1 if you have the `m' library (-lm). */
#undef HAVE_LIBM
--- a/configure
+++ b/configure
@@ -22122,6 +22122,14 @@ $as_echo "$as_me: checking types, headers, and functions" >&6;}
# We must check for all these, because they may be used by the netCDF
# C library.
+# Removing the checks for some of the libraries because of issues
+# observed when they are detected, are not needed, and an attempt to
+# link against is made anyways.
+# See https://github.com/Unidata/netcdf-fortran/issues/164
+#
+# Specifying LDFLAGS="$(nc-config --libs [--static])" should
+# let downstream developers link more reliably against libnetcdf.
+
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for floor in -lm" >&5
$as_echo_n "checking for floor in -lm... " >&6; }
if ${ac_cv_lib_m_floor+:} false; then :
@@ -22167,163 +22175,6 @@ _ACEOF
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for curl_easy_setopt in -lcurl" >&5
-$as_echo_n "checking for curl_easy_setopt in -lcurl... " >&6; }
-if ${ac_cv_lib_curl_curl_easy_setopt+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- ac_check_lib_save_LIBS=$LIBS
-LIBS="-lcurl $LIBS"
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char curl_easy_setopt ();
-int
-main ()
-{
-return curl_easy_setopt ();
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
- ac_cv_lib_curl_curl_easy_setopt=yes
-else
- ac_cv_lib_curl_curl_easy_setopt=no
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
-LIBS=$ac_check_lib_save_LIBS
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_curl_curl_easy_setopt" >&5
-$as_echo "$ac_cv_lib_curl_curl_easy_setopt" >&6; }
-if test "x$ac_cv_lib_curl_curl_easy_setopt" = xyes; then :
- cat >>confdefs.h <<_ACEOF
-#define HAVE_LIBCURL 1
-_ACEOF
-
- LIBS="-lcurl $LIBS"
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing deflate" >&5
-$as_echo_n "checking for library containing deflate... " >&6; }
-if ${ac_cv_search_deflate+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- ac_func_search_save_LIBS=$LIBS
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char deflate ();
-int
-main ()
-{
-return deflate ();
- ;
- return 0;
-}
-_ACEOF
-for ac_lib in '' zlibwapi zlibstat zlib zlib1 z; do
- if test -z "$ac_lib"; then
- ac_res="none required"
- else
- ac_res=-l$ac_lib
- LIBS="-l$ac_lib $ac_func_search_save_LIBS"
- fi
- if ac_fn_c_try_link "$LINENO"; then :
- ac_cv_search_deflate=$ac_res
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext
- if ${ac_cv_search_deflate+:} false; then :
- break
-fi
-done
-if ${ac_cv_search_deflate+:} false; then :
-
-else
- ac_cv_search_deflate=no
-fi
-rm conftest.$ac_ext
-LIBS=$ac_func_search_save_LIBS
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_deflate" >&5
-$as_echo "$ac_cv_search_deflate" >&6; }
-ac_res=$ac_cv_search_deflate
-if test "$ac_res" != no; then :
- test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing SZ_Compress" >&5
-$as_echo_n "checking for library containing SZ_Compress... " >&6; }
-if ${ac_cv_search_SZ_Compress+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- ac_func_search_save_LIBS=$LIBS
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char SZ_Compress ();
-int
-main ()
-{
-return SZ_Compress ();
- ;
- return 0;
-}
-_ACEOF
-for ac_lib in '' szip sz; do
- if test -z "$ac_lib"; then
- ac_res="none required"
- else
- ac_res=-l$ac_lib
- LIBS="-l$ac_lib $ac_func_search_save_LIBS"
- fi
- if ac_fn_c_try_link "$LINENO"; then :
- ac_cv_search_SZ_Compress=$ac_res
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext
- if ${ac_cv_search_SZ_Compress+:} false; then :
- break
-fi
-done
-if ${ac_cv_search_SZ_Compress+:} false; then :
-
-else
- ac_cv_search_SZ_Compress=no
-fi
-rm conftest.$ac_ext
-LIBS=$ac_func_search_save_LIBS
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_SZ_Compress" >&5
-$as_echo "$ac_cv_search_SZ_Compress" >&6; }
-ac_res=$ac_cv_search_SZ_Compress
-if test "$ac_res" != no; then :
- test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
-
-fi
-
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dlopen" >&5
$as_echo_n "checking for library containing dlopen... " >&6; }
if ${ac_cv_search_dlopen+:} false; then :
@@ -22380,118 +22231,6 @@ if test "$ac_res" != no; then :
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing H5Fflush" >&5
-$as_echo_n "checking for library containing H5Fflush... " >&6; }
-if ${ac_cv_search_H5Fflush+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- ac_func_search_save_LIBS=$LIBS
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char H5Fflush ();
-int
-main ()
-{
-return H5Fflush ();
- ;
- return 0;
-}
-_ACEOF
-for ac_lib in '' hdf5dll hdf5; do
- if test -z "$ac_lib"; then
- ac_res="none required"
- else
- ac_res=-l$ac_lib
- LIBS="-l$ac_lib $ac_func_search_save_LIBS"
- fi
- if ac_fn_c_try_link "$LINENO"; then :
- ac_cv_search_H5Fflush=$ac_res
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext
- if ${ac_cv_search_H5Fflush+:} false; then :
- break
-fi
-done
-if ${ac_cv_search_H5Fflush+:} false; then :
-
-else
- ac_cv_search_H5Fflush=no
-fi
-rm conftest.$ac_ext
-LIBS=$ac_func_search_save_LIBS
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_H5Fflush" >&5
-$as_echo "$ac_cv_search_H5Fflush" >&6; }
-ac_res=$ac_cv_search_H5Fflush
-if test "$ac_res" != no; then :
- test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing H5DSis_scale" >&5
-$as_echo_n "checking for library containing H5DSis_scale... " >&6; }
-if ${ac_cv_search_H5DSis_scale+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- ac_func_search_save_LIBS=$LIBS
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char H5DSis_scale ();
-int
-main ()
-{
-return H5DSis_scale ();
- ;
- return 0;
-}
-_ACEOF
-for ac_lib in '' hdf5_hldll hdf5_hl; do
- if test -z "$ac_lib"; then
- ac_res="none required"
- else
- ac_res=-l$ac_lib
- LIBS="-l$ac_lib $ac_func_search_save_LIBS"
- fi
- if ac_fn_c_try_link "$LINENO"; then :
- ac_cv_search_H5DSis_scale=$ac_res
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext
- if ${ac_cv_search_H5DSis_scale+:} false; then :
- break
-fi
-done
-if ${ac_cv_search_H5DSis_scale+:} false; then :
-
-else
- ac_cv_search_H5DSis_scale=no
-fi
-rm conftest.$ac_ext
-LIBS=$ac_func_search_save_LIBS
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_H5DSis_scale" >&5
-$as_echo "$ac_cv_search_H5DSis_scale" >&6; }
-ac_res=$ac_cv_search_H5DSis_scale
-if test "$ac_res" != no; then :
- test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
-
-fi
-
# Find the netCDF header and library.
for ac_header in netcdf.h

13
var/spack/repos/builtin/packages/netcdf-fortran/logging.patch Normal file
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@ -0,0 +1,13 @@
--- a/fortran/nf_logging.F90
+++ b/fortran/nf_logging.F90
@@ -1,3 +1,10 @@
+! This file is compiled only if logging is enabled. However, the macro LOGGING
+! is never defined. For most of the compilers this simply leads to an empty
+! object: they do not complain when a source file is empty. This is not the
+! case for NAG: the compiler fails the compilation of empty sources. To fix
+! this problem, we define the macro here.
+#define LOGGING
+
#ifdef LOGGING
! Function to turn on logging
!-------------------------------- nf_set_log_level ----------------------------

31
var/spack/repos/builtin/packages/netcdf-fortran/nag.patch
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@ -1,31 +0,0 @@
diff --git a/configure b/configure
index 06ac8b0..d518a1a 100755
--- a/configure
+++ b/configure
@@ -10657,6 +10657,8 @@ _LT_EOF
lf95*) # Lahey Fortran 8.1
whole_archive_flag_spec=
tmp_sharedflag='--shared' ;;
+ nagfor*)
+ tmp_sharedflag='-Wl,-shared' ;;
xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
tmp_sharedflag='-qmkshrobj'
tmp_addflag= ;;
@@ -14252,6 +14254,8 @@ _LT_EOF
lf95*) # Lahey Fortran 8.1
whole_archive_flag_spec_F77=
tmp_sharedflag='--shared' ;;
+ nagfor*)
+ tmp_sharedflag='-Wl,-shared' ;;
xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
tmp_sharedflag='-qmkshrobj'
tmp_addflag= ;;
@@ -17142,6 +17146,8 @@ _LT_EOF
lf95*) # Lahey Fortran 8.1
whole_archive_flag_spec_FC=
tmp_sharedflag='--shared' ;;
+ nagfor*)
+ tmp_sharedflag='-Wl,-shared' ;;
xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
tmp_sharedflag='-qmkshrobj'
tmp_addflag= ;;

124
var/spack/repos/builtin/packages/netcdf-fortran/nag_libtool_2.4.2.patch Normal file
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@ -0,0 +1,124 @@
--- a/configure
+++ b/configure
@@ -9584,6 +9584,10 @@ for cc_temp in $compiler""; do
esac
done
cc_basename=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
+case $cc_basename in
+ nagfor*) ;;
+ *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && cc_basename='nagfor-wrapper' ;;
+esac
# Only perform the check for file, if the check method requires it
@@ -10657,6 +10661,10 @@ _LT_EOF
lf95*) # Lahey Fortran 8.1
whole_archive_flag_spec=
tmp_sharedflag='--shared' ;;
+ nagfor*)
+ whole_archive_flag_spec='${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'
tmp_addflag= ;;
@@ -13415,6 +13423,10 @@ $RM -r conftest*
esac
done
cc_basename=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
+case $cc_basename in
+ nagfor*) ;;
+ *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && cc_basename='nagfor-wrapper' ;;
+esac
GCC=$G77
if test -n "$compiler"; then
@@ -14252,6 +14264,10 @@ _LT_EOF
lf95*) # Lahey Fortran 8.1
whole_archive_flag_spec_F77=
tmp_sharedflag='--shared' ;;
+ nagfor*)
+ whole_archive_flag_spec_F77='${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'
tmp_addflag= ;;
@@ -16142,6 +16158,10 @@ $RM -r conftest*
esac
done
cc_basename=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
+case $cc_basename in
+ nagfor*) ;;
+ *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && cc_basename='nagfor-wrapper' ;;
+esac
if test -n "$compiler"; then
@@ -17142,6 +17162,10 @@ _LT_EOF
lf95*) # Lahey Fortran 8.1
whole_archive_flag_spec_FC=
tmp_sharedflag='--shared' ;;
+ nagfor*)
+ 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\"` ${wl}--no-whole-archive'
+ compiler_needs_object_FC=yes
+ tmp_sharedflag='-Wl,-shared' ;;
xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
tmp_sharedflag='-qmkshrobj'
tmp_addflag= ;;
--- a/ltmain.sh
+++ b/ltmain.sh
@@ -180,6 +180,24 @@ func_basename ()
func_basename_result=`$ECHO "${1}" | $SED "$basename"`
} # func_basename may be replaced by extended shell implementation
+# Calculate cc_basename. Skip known compiler wrappers and cross-prefix.
+func_cc_basename ()
+{
+ for cc_temp in $*""; do
+ case $cc_temp in
+ compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+ distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+ \-*) ;;
+ *) break;;
+ esac
+ done
+ func_cc_basename_result=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
+ case $func_cc_basename_result in
+ nagfor*) ;;
+ *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && func_cc_basename_result='nagfor-wrapper' ;;
+ esac
+}
+
# func_dirname_and_basename file append nondir_replacement
# perform func_basename and func_dirname in a single function
@@ -6422,6 +6440,13 @@ func_mode_link ()
# Convert "-framework foo" to "foo.ltframework"
if test -n "$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 "*) ;;
@@ -8007,6 +8032,14 @@ 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=

96
var/spack/repos/builtin/packages/netcdf-fortran/nag_libtool_2.4.6.patch Normal file
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@ -0,0 +1,96 @@
--- a/configure
+++ b/configure
@@ -9034,6 +9034,12 @@ func_cc_basename ()
esac
done
func_cc_basename_result=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
+
+ # Set result to 'nagfor-wrapper' when NAG compiler is called via a wrapper (e.g. mpif90).
+ case $func_cc_basename_result in
+ nagfor*) ;;
+ *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && func_cc_basename_result='nagfor-wrapper' ;;
+ esac
}
# Check whether --enable-libtool-lock was given.
@@ -11811,6 +11817,8 @@ _LT_EOF
whole_archive_flag_spec=
tmp_sharedflag='--shared' ;;
nagfor*) # NAGFOR 5.3
+ whole_archive_flag_spec='$wl--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
+ compiler_needs_object=yes
tmp_sharedflag='-Wl,-shared' ;;
xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
tmp_sharedflag='-qmkshrobj'
@@ -15663,6 +15671,8 @@ _LT_EOF
whole_archive_flag_spec_F77=
tmp_sharedflag='--shared' ;;
nagfor*) # NAGFOR 5.3
+ whole_archive_flag_spec_F77='$wl--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
+ compiler_needs_object_F77=yes
tmp_sharedflag='-Wl,-shared' ;;
xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
tmp_sharedflag='-qmkshrobj'
@@ -18788,6 +18798,8 @@ _LT_EOF
whole_archive_flag_spec_FC=
tmp_sharedflag='--shared' ;;
nagfor*) # NAGFOR 5.3
+ whole_archive_flag_spec_FC='$wl--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
+ compiler_needs_object_FC=yes
tmp_sharedflag='-Wl,-shared' ;;
xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
tmp_sharedflag='-qmkshrobj'
@@ -26086,6 +26098,12 @@ func_cc_basename ()
esac
done
func_cc_basename_result=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
+
+ # Set result to 'nagfor-wrapper' when NAG compiler is called via a wrapper (e.g. mpif90).
+ case $func_cc_basename_result in
+ nagfor*) ;;
+ *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && func_cc_basename_result='nagfor-wrapper' ;;
+ esac
}
--- a/ltmain.sh
+++ b/ltmain.sh
@@ -7868,6 +7868,13 @@ func_mode_link ()
# Convert "-framework foo" to "foo.ltframework"
if test -n "$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
*" $tmp_inherited_linker_flag "*) ;;
@@ -8890,7 +8897,8 @@ func_mode_link ()
xlcverstring="$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"
;;
@@ -9502,6 +9510,14 @@ 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=

11
var/spack/repos/builtin/packages/netcdf-fortran/nag_testing.patch Normal file
View File

@ -0,0 +1,11 @@
--- a/nf_test/ftst_rengrps.F
+++ b/nf_test/ftst_rengrps.F
@@ -11,7 +11,7 @@ C use typeSizes
C use netcdf
C use netcdf4_f03
implicit none
- include "netcdf.inc"
+ include "netcdf.inc"
C This is the name of the data file we will create.
character (len = *), parameter :: FILE_NAME = "ftst_rengrps.nc"

67
var/spack/repos/builtin/packages/netcdf-fortran/package.py
View File

@ -13,7 +13,9 @@ class NetcdfFortran(AutotoolsPackage):
distribution.""" distribution."""
homepage = "https://www.unidata.ucar.edu/software/netcdf" homepage = "https://www.unidata.ucar.edu/software/netcdf"
url = "https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.5.2.tar.gz" url = "https://www.gfd-dennou.org/arch/netcdf/unidata-mirror/netcdf-fortran-4.5.2.tar.gz"
maintainers = ['skosukhin']
version('4.5.2', sha256='b959937d7d9045184e9d2040a915d94a7f4d0185f4a9dceb8f08c94b0c3304aa') version('4.5.2', sha256='b959937d7d9045184e9d2040a915d94a7f4d0185f4a9dceb8f08c94b0c3304aa')
version('4.4.5', sha256='2467536ce29daea348c736476aa8e684c075d2f6cab12f3361885cb6905717b8') version('4.4.5', sha256='2467536ce29daea348c736476aa8e684c075d2f6cab12f3361885cb6905717b8')
@ -24,6 +26,7 @@ class NetcdfFortran(AutotoolsPackage):
description='Enable parallel I/O for netcdf-4') description='Enable parallel I/O for netcdf-4')
variant('pic', default=True, variant('pic', default=True,
description='Produce position-independent code (for shared libs)') description='Produce position-independent code (for shared libs)')
variant('shared', default=True, description='Enable shared library')
# We need to build with MPI wrappers if parallel I/O features is enabled: # We need to build with MPI wrappers if parallel I/O features is enabled:
# https://www.unidata.ucar.edu/software/netcdf/docs/building_netcdf_fortran.html # https://www.unidata.ucar.edu/software/netcdf/docs/building_netcdf_fortran.html
@ -34,42 +37,79 @@ class NetcdfFortran(AutotoolsPackage):
# The default libtool.m4 is too old to handle NAG compiler properly: # The default libtool.m4 is too old to handle NAG compiler properly:
# https://github.com/Unidata/netcdf-fortran/issues/94 # https://github.com/Unidata/netcdf-fortran/issues/94
patch('nag.patch', when='@:4.4.4%nag') # Moreover, Libtool can't handle '-pthread' flag coming from libcurl,
# doesn't inject convenience libraries into the shared ones, and is unable
# to detect NAG when it is called with an MPI wrapper.
patch('nag_libtool_2.4.2.patch', when='@:4.4.4%nag')
patch('nag_libtool_2.4.6.patch', when='@4.4.5:%nag')
# Enable 'make check' for NAG, which is too strict.
patch('nag_testing.patch', when='@4.4.5%nag')
# File fortran/nf_logging.F90 is compiled without -DLOGGING, which leads
# to missing symbols in the library. Additionally, the patch enables
# building with NAG, which refuses to compile empty source files (see also
# comments in the patch):
patch('logging.patch', when='@:4.4.5')
# Prevent excessive linking to system libraries. Without this patch the
# library might get linked to the system installation of libcurl. See
# https://github.com/Unidata/netcdf-fortran/commit/0a11f580faebbc1c4dce68bf5135709d1c7c7cc1#diff-67e997bcfdac55191033d57a16d1408a
patch('excessive_linking.patch', when='@4.4.5')
# Parallel builds do not work in the fortran directory. This patch is # Parallel builds do not work in the fortran directory. This patch is
# derived from https://github.com/Unidata/netcdf-fortran/pull/211 # derived from https://github.com/Unidata/netcdf-fortran/pull/211
patch('no_parallel_build.patch', when='@4.5.2') patch('no_parallel_build.patch', when='@4.5.2')
def flag_handler(self, name, flags): def flag_handler(self, name, flags):
config_flags = None
if name in ['cflags', 'fflags'] and '+pic' in self.spec: if name in ['cflags', 'fflags'] and '+pic' in self.spec:
flags.append(self.compiler.pic_flag) # Unlike NetCDF-C, we add PIC flag only when +pic. Adding the
# flags also when ~shared would make it impossible to build a
# static-only version of the library with NAG.
config_flags = [self.compiler.pic_flag]
elif name == 'cppflags': elif name == 'cppflags':
flags.append(self.spec['netcdf-c'].headers.cpp_flags) config_flags = [self.spec['netcdf-c'].headers.cpp_flags]
elif name == 'ldflags': elif name == 'ldflags':
# We need to specify LDFLAGS to get correct dependency_libs # We need to specify LDFLAGS to get correct dependency_libs
# in libnetcdff.la, so packages that use libtool for linking # in libnetcdff.la, so packages that use libtool for linking
# could correctly link to all the dependencies even when the # could correctly link to all the dependencies even when the
# building takes place outside of Spack environment, i.e. # building takes place outside of Spack environment, i.e.
# without Spack's compiler wrappers. # without Spack's compiler wrappers.
flags.append(self.spec['netcdf-c'].libs.search_flags) config_flags = [self.spec['netcdf-c'].libs.search_flags]
return None, None, flags return flags, None, config_flags
@property @property
def libs(self): def libs(self):
libraries = ['libnetcdff'] libraries = ['libnetcdff']
# This package installs both shared and static libraries. Permit
# clients to query which one they want.
query_parameters = self.spec.last_query.extra_parameters query_parameters = self.spec.last_query.extra_parameters
shared = 'shared' in query_parameters
return find_libraries( if 'shared' in query_parameters:
shared = True
elif 'static' in query_parameters:
shared = False
else:
shared = '+shared' in self.spec
libs = find_libraries(
libraries, root=self.prefix, shared=shared, recursive=True libraries, root=self.prefix, shared=shared, recursive=True
) )
if libs:
return libs
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))
def configure_args(self): def configure_args(self):
config_args = [] config_args = self.enable_or_disable('shared')
config_args.append('--enable-static')
if '+mpi' in self.spec: if '+mpi' in self.spec:
config_args.append('CC=%s' % self.spec['mpi'].mpicc) config_args.append('CC=%s' % self.spec['mpi'].mpicc)
@ -77,3 +117,8 @@ def configure_args(self):
config_args.append('F77=%s' % self.spec['mpi'].mpif77) config_args.append('F77=%s' % self.spec['mpi'].mpif77)
return config_args return config_args
@when('@:4.4.5')
def check(self):
with working_dir(self.build_directory):
make('check', parallel=False)