[Trilinos-Users] Trilinos Compilation Error on Linux

John T. Foster jfoster at austin.utexas.edu
Mon Jun 6 14:35:31 EDT 2016 

Some of those flags are specific to Intel compilers.  Again, my advice
would be to compile openmpi against the correct Intel compilers.

JTF

On Mon, Jun 6, 2016 at 1:29 PM, Sai P Uppati <uppatis at utexas.edu> wrote:

> John,
>
> There is another OpenMPI module version 1.10.2 that is based on GNU
> compilers version 4.7.3. When I load this module, the mpicc and mpicxx wrap
> gcc and g++ compilers, respectively, which is correct. However, when I
> try and configure the Trilinos build with the a very similar cmake script
> as your stampede one on GitHub Gists, I have problems with some of the
> CMAKE C and CXX flags:
>
> Building C object CMakeFiles/cmTC_a870f.dir/testCCompiler.c.o
>
>   /software/openmpi/PBS/1.10.2/gcc_47/bin/mpicc -O2 -Wall -ansi
>   -Wno-long-long -fp-model precise -fp-model source -ip -xHost -I/include
>   -I/home/de566876/projects/netcdf/include -o
>   CMakeFiles/cmTC_a870f.dir/testCCompiler.c.o -c
>
> /home/de566876/source_codes/Trilinos/build/CMakeFiles/CMakeTmp/testCCompiler.c
>
>
>   gcc: error: unrecognized command line option ‘-fp-model’
>
>   gcc: error: precise: No such file or directory
>
>   gcc: error: unrecognized command line option ‘-fp-model’
>
>   gcc: error: source: No such file or directory
>
>   gcc: error: unrecognized command line option ‘-ip’
>
>   gmake[1]: *** [CMakeFiles/cmTC_a870f.dir/testCCompiler.c.o] Error 1
>
>   gmake[1]: Leaving directory
>   `/home/de566876/source_codes/Trilinos/build/CMakeFiles/CMakeTmp'
>
>   gmake: *** [cmTC_a870f/fast] Error 2
>
> I wonder if these flags are essential. If they are, what could be causing
> these errors in the configuration?
>
> Sai
>
> On Mon, Jun 6, 2016 at 1:13 PM, John T. Foster <jfoster at austin.utexas.edu>
> wrote:
>
>> You probably need to rebuild openmpi setting the variable CXX=icpc at
>> configuration.
>>
>> JTF
>> ​
>>
>> On Mon, Jun 6, 2016 at 1:07 PM, Sai P Uppati <uppatis at utexas.edu> wrote:
>>
>>> It looks like the mpicxx wrapper wraps icc again, NOT icpc.
>>>
>>> mpicc -show returns:
>>>
>>> icc -I/software/openmpi/PBS/1.10.2/intel_16/include -pthread
>>> -L/software/PBSpro/default//lib -Wl,-rpath
>>> -Wl,/software/PBSpro/default//lib -Wl,-rpath
>>> -Wl,/software/openmpi/PBS/1.10.2/intel_16/lib -Wl,--enable-new-dtags
>>> -L/software/openmpi/PBS/1.10.2/intel_16/lib -lmpi
>>>
>>> mpicxx -show returns:
>>>
>>> icc -I/software/openmpi/PBS/1.10.2/intel_16/include -pthread
>>> -L/software/PBSpro/default//lib -Wl,-rpath
>>> -Wl,/software/PBSpro/default//lib -Wl,-rpath
>>> -Wl,/software/openmpi/PBS/1.10.2/intel_16/lib -Wl,--enable-new-dtags
>>> -L/software/openmpi/PBS/1.10.2/intel_16/lib -lmpi_cxx -lmpi
>>>
>>> If I type in ic and hit TAB, in the results, both icc and icpc are
>>> found. It just looks like icpc is unused. Is this something I can do a
>>> simple workaround for? Or do I need to ask the system admins to fix the
>>> wrappers?
>>>
>>> Sai
>>>
>>> On Mon, Jun 6, 2016 at 12:55 PM, John T. Foster <
>>> jfoster at austin.utexas.edu> wrote:
>>>
>>>> Sai,
>>>>
>>>> What does mpicxx -show return? It should be wrapping icpc.
>>>>
>>>> JTF
>>>> ​
>>>>
>>>> On Mon, Jun 6, 2016 at 12:47 PM, Heroux, Mike <MHeroux at csbsju.edu>
>>>> wrote:
>>>>
>>>>> It looks like you are compiling C++ with a C compiler.  This will not
>>>>> work.
>>>>>
>>>>>
>>>>>
>>>>> Mike
>>>>>
>>>>>
>>>>>
>>>>> *From: *Trilinos-Users <trilinos-users-bounces at trilinos.org> on
>>>>> behalf of Sai P Uppati <uppatis at utexas.edu>
>>>>> *Date: *Monday, June 6, 2016 at 10:26 AM
>>>>> *To: *"John T. Foster" <jfoster at austin.utexas.edu>
>>>>> *Cc: *Roscoe Bartlett <rabartl at sandia.gov>, Trilinos Users <
>>>>> trilinos-users at trilinos.org>
>>>>> *Subject: *Re: [Trilinos-Users] [EXTERNAL] Trilinos Compilation Error
>>>>> on Linux
>>>>>
>>>>>
>>>>>
>>>>> I didn't notice before I think, but I'm getting other errors as well,
>>>>> besides the one I showed. Examples include:
>>>>>
>>>>>
>>>>>
>>>>> [  0%] Building C object
>>>>> packages/seacas/libraries/chaco/CMakeFiles/chaco.dir/assign/assign_out.c.o
>>>>>
>>>>> In file included from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/KokkosExp_View.hpp(53),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_View.hpp(2104),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_Parallel.hpp(52),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_Serial.hpp(52),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_Core.hpp(53),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/impl/KokkosExp_SharedAlloc.cpp(44):
>>>>>
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_HostSpace.hpp(160):
>>>>> *error*: invalid type for defaulted constructor
>>>>>
>>>>>     HostSpace( HostSpace && rhs ) = default ;
>>>>>
>>>>>     ^
>>>>>
>>>>>
>>>>>
>>>>> In file included from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/KokkosExp_View.hpp(53),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_View.hpp(2104),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_Parallel.hpp(52),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_Serial.hpp(52),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_Core.hpp(53),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/impl/KokkosExp_SharedAlloc.cpp(44):
>>>>>
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_HostSpace.hpp(162):
>>>>> *error*: invalid type for defaulted assignment operator
>>>>>
>>>>>     HostSpace & operator = ( HostSpace && ) = default ;
>>>>>
>>>>>                 ^
>>>>>
>>>>>
>>>>>
>>>>> In file included from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/KokkosExp_View.hpp(55),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_View.hpp(2104),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_Parallel.hpp(52),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_Serial.hpp(52),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_Core.hpp(53),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/impl/KokkosExp_SharedAlloc.cpp(44):
>>>>>
>>>>> /home/de566876/source_codes/Trilinos/packages/kokkos/core/src/Kokkos_ExecPolicy.hpp(259):
>>>>> *error*: invalid type for defaulted constructor
>>>>>
>>>>>     RangePolicy(RangePolicy&&) = default;
>>>>>
>>>>>     ^
>>>>>
>>>>>
>>>>>
>>>>> Is this also a compiler issue? The error with the netcdf.h with the
>>>>> comment beginning with "//" is still there as well. Any idea what the
>>>>> problem could be?
>>>>>
>>>>>
>>>>>
>>>>> Sai
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Jun 6, 2016 at 9:25 AM, Sai P Uppati <uppatis at utexas.edu>
>>>>> wrote:
>>>>>
>>>>> Ross, sorry I misunderstood. John, thanks for that clarification. It
>>>>> looks like I was using
>>>>>
>>>>>
>>>>>
>>>>> icc version 15.0.1 (gcc version 4.7.3 compatibility)
>>>>>
>>>>>
>>>>>
>>>>> And I changed to
>>>>>
>>>>>
>>>>>
>>>>> icc version 16.0.2 (gcc version 4.4.7 compatibility)
>>>>>
>>>>>
>>>>>
>>>>> Both of them are having the same issue.
>>>>>
>>>>>
>>>>>
>>>>> Sai
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Jun 6, 2016 at 8:48 AM, John T. Foster <
>>>>> jfoster at austin.utexas.edu> wrote:
>>>>>
>>>>> Sai,
>>>>>
>>>>> mpicc and mpicxx are just wrappers on the underlying compilers which
>>>>> are most likely some version of gcc. You can see the full compiler
>>>>> and linker command with mpicc -show. If the underlying compiler is in
>>>>> fact gcc, you can see the version with gcc -v.
>>>>>
>>>>> JTF
>>>>>
>>>>> ​
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Jun 6, 2016 at 8:20 AM, Sai P Uppati <uppatis at utexas.edu>
>>>>> wrote:
>>>>>
>>>>> Hi Ross,
>>>>>
>>>>>
>>>>>
>>>>> It looks like I'm using mpicc, mpicxx compilers from the OpemMPI 1.6.5
>>>>> version. Are these too old for compiling the latest version of Trilinos?
>>>>>
>>>>>
>>>>>
>>>>> Sai
>>>>>
>>>>>
>>>>>
>>>>> On Sat, Jun 4, 2016 at 9:15 PM, Bartlett, Roscoe A <rabartl at sandia.gov>
>>>>> wrote:
>>>>>
>>>>> Looks like your C compiler is not accepting C99 code.  C89 does not
>>>>> accept // as a comment.  What C compiler are you using?
>>>>>
>>>>> -Ross
>>>>> ------------------------------
>>>>>
>>>>> *From:* Trilinos-Users <trilinos-users-bounces at trilinos.org> on
>>>>> behalf of Sai P Uppati <uppatis at utexas.edu>
>>>>> *Sent:* Saturday, June 4, 2016 5:37:29 PM
>>>>> *To:* trilinos-users at trilinos.org; trilinos-users at software.sandia.gov
>>>>> *Subject:* [EXTERNAL] [Trilinos-Users] Trilinos Compilation Error on
>>>>> Linux
>>>>>
>>>>>
>>>>>
>>>>> Hi,
>>>>>
>>>>>
>>>>>
>>>>> I'm trying to compile Trilinos (latest version: GitHub version) on a
>>>>> Linux Red Hat distribution, and I'm getting a compilation error regarding
>>>>> netcdf.h:
>>>>>
>>>>>
>>>>>
>>>>> Building C object
>>>>> packages/seacas/libraries/supes/CMakeFiles/supes.dir/ext_lib/exmemy.c.o
>>>>>
>>>>> /home/de566876/source_codes/Trilinos/packages/seacas/libraries/exodus/src/ex_close.c(50):
>>>>> warning #14: extra text after expected end of preprocessing directive
>>>>>
>>>>>   #include "exodusII.h"     // for ex_err, exerrval, etc
>>>>>
>>>>>                             ^
>>>>>
>>>>>
>>>>>
>>>>> In file included from
>>>>> /home/de566876/source_codes/Trilinos/packages/seacas/libraries/exodus/include/exodusII.h(46),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/seacas/libraries/exodus/src/ex_add_attr.c(35):
>>>>>
>>>>> /home/de566876/projects/netcdf/include/netcdf.h(1951): error: expected
>>>>> a declaration
>>>>>
>>>>>     //EXTERNL int nc_finalize();
>>>>>
>>>>>     ^
>>>>>
>>>>>
>>>>>
>>>>> [  5%] In file included from
>>>>> /home/de566876/source_codes/Trilinos/packages/seacas/libraries/exodus/include/exodusII.h(46),
>>>>>
>>>>>                  from
>>>>> /home/de566876/source_codes/Trilinos/packages/seacas/libraries/exodus/src/ex_close.c(50):
>>>>>
>>>>> /home/de566876/projects/netcdf/include/netcdf.h(1951): error: expected
>>>>> a declaration
>>>>>
>>>>>     //EXTERNL int nc_finalize();
>>>>>
>>>>>     ^
>>>>>
>>>>>
>>>>>
>>>>> Does this error have to do with the netcdf build (version 4.4.0, which
>>>>> passed all the tests in the test suite by the way)?
>>>>>
>>>>>
>>>>>
>>>>> Sincerely,
>>>>>
>>>>> Sai Uppati
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> [image: mage removed by sender.]ᐧ
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Trilinos-Users mailing list
>>>>> Trilinos-Users at trilinos.org
>>>>> https://trilinos.org/mailman/listinfo/trilinos-users
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Trilinos-Users mailing list
>>>>> Trilinos-Users at trilinos.org
>>>>> https://trilinos.org/mailman/listinfo/trilinos-users
>>>>>
>>>>>
>>>>
>>>
>>> _______________________________________________
>>> Trilinos-Users mailing list
>>> Trilinos-Users at trilinos.org
>>> https://trilinos.org/mailman/listinfo/trilinos-users
>>>
>>>
>>
>
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