[netCDF #PQU-107704]: Building NetCDF-cxx4 4.2.1 with PGI and mvapich2

Hi Chris,

Thanks for your bug report and workaround!

I've created a Jira issue tracking report with the details you provided, as 
well as a link
to the patch for the generated libtool that you created as a workaround:

  https://bugtracking.unidata.ucar.edu/browse/NCXXF-11

For now, I hope that will help other users  find your solution in case they who 
encounter 
the same problem.

--Russ

> There appears to be some kind of problem in the NetCDF-cxx4 build system when 
> using PGI and mvapich2 to link against a NetCDF 4.3.0 that was built with 
> --enable-parallel-test.  I am using the latest stable release (4.2.1) of 
> NetCDF-cxx4, PGI versions 12.5-0 and/or 13.2-0, and mvapich2 version 1.8.  I 
> can configure and build NetCDF-cxx4 using a NetCDF that was built either with 
> or without parallel support using the Intel compilers.  And I can configure 
> and build NetCDF-cxx4 with PGI for a non-parallel build.  To be specific, the 
> problem is that the build refuses to produce a shared library for NetCDF-cxx4 
> when using mpicxx (MPI wrapper for pgCC) for the C++ compiler.
> 
> The problem seems to be that, for whatever reason, it does not know how to 
> correctly recognize/test for shared library.  The libtool that is generated 
> won't create the shared library for NetCDF-cxx4 but the "configure" and 
> "make" steps do run fine and produce a static library.  The "make check" then 
> fails because it tries to link to a non-existent shared library.
> 
> I have been able to work around this problem for now by applying the 
> following patch to the libtool that is generated when configuring 
> NetCDF-cxx4, but am wondering if there might be some underlying problem that 
> needs fixing.  Applying that patch allows "make" and "make check" to work 
> without generating errors.
> 
> While I did do quite a lot of searching for other reports of this problem I 
> did not find anything.  Any advice or comments regarding the appropriateness 
> of my libtool patch or a better solution would be much appreciated.
> 
> 
> --- build/netcdf-cxx4-mvapich2/4.2.1/pgi/12.5-0/mvapich2/1.8/libtool  
> 2014-01-10 20:01:32.000000000 +0000
> +++ build/netcdf-cxx4/4.2.1/pgi/12.5-0/libtool        2014-01-10 
> 20:19:33.000000000 +0000
> @@ -332,7 +332,7 @@
> export_dynamic_flag_spec="\${wl}--export-dynamic"
> 
> # Compiler flag to generate shared objects directly from archives.
> -whole_archive_flag_spec="\${wl}--whole-archive\$convenience 
> \${wl}--no-whole-archive"
> +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"
> 
> # Whether the compiler copes with passing no objects directly.
> compiler_needs_object="no"
> @@ -10113,10 +10113,10 @@
> no_builtin_flag=""
> 
> # Additional compiler flags for building library objects.
> -pic_flag=" -DPIC"
> +pic_flag=" -fpic -DPIC"
> 
> # How to pass a linker flag through the compiler.
> -wl=""
> +wl="-Wl,"
> 
> # Compiler flag to prevent dynamic linking.
> link_static_flag=""
> @@ -10131,10 +10131,10 @@
> allow_libtool_libs_with_static_runtimes=no
> 
> # Compiler flag to allow reflexive dlopens.
> -export_dynamic_flag_spec=""
> +export_dynamic_flag_spec="\${wl}--export-dynamic"
> 
> # Compiler flag to generate shared objects directly from archives.
> -whole_archive_flag_spec=""
> +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"
> 
> # Whether the compiler copes with passing no objects directly.
> compiler_needs_object="no"
> @@ -10146,8 +10146,8 @@
> old_archive_from_expsyms_cmds=""
> 
> # Commands used to build a shared archive.
> -archive_cmds=""
> -archive_expsym_cmds=""
> +archive_cmds="\$CC -shared \$pic_flag \$predep_objects \$libobjs \$deplibs 
> \$postdep_objects \$compiler_flags \${wl}-soname \${wl}\$soname -o \$lib"
> +archive_expsym_cmds="\$CC -shared \$pic_flag \$predep_objects \$libobjs 
> \$deplibs \$postdep_objects \$compiler_flags \${wl}-soname \${wl}\$soname 
> \${wl}-retain-symbols-file \${wl}\$export_symbols -o \$lib"
> 
> # Commands used to build a loadable module if different from building
> # a shared archive.
> @@ -10165,7 +10165,7 @@
> 
> # Flag to hardcode $libdir into a binary during linking.
> # This must work even if $libdir does not exist
> -hardcode_libdir_flag_spec=""
> +hardcode_libdir_flag_spec="\${wl}--rpath \${wl}\$libdir"
> 
> # Whether we need a single "-rpath" flag with a separated argument.
> hardcode_libdir_separator=""
> @@ -10222,7 +10222,7 @@
> file_list_spec=""
> 
> # How to hardcode a shared library path into an executable.
> -hardcode_action=unsupported
> +hardcode_action=immediate
> 
> # The directories searched by this compiler when creating a shared library.
> compiler_lib_search_dirs=""
> 
> ## End of patch
> 
> 
> 
> Thank you for your consideration,
> 
> 
> Chris
> -----------------------------------------------------------------------------------------------------------
> Christopher W. Harrop                               email: address@hidden
> Global Systems Division                                                       
>    voice: (303) 497-6808
> NOAA Earth System Research Laboratory                               fax: 
> (303) 497-7259
> 325 Broadway R/GSD2
> Boulder, CO 80303
> 
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: PQU-107704
Department: Support netCDF
Priority: High
Status: Closed