[Trilinos-Users] Trilinos Compilation Error on Linux

Sai P Uppati uppatis at utexas.edu
Mon Jun 6 14:43:34 EDT 2016 

I've never tried building OpenMPI myself I think. Is it a big undertaking?
If so, I can request it to be correctly built this time by the system
admins.

If not, I can give it a shot myself.

Sai

On Mon, Jun 6, 2016 at 1:35 PM, John T. Foster <jfoster at austin.utexas.edu>
wrote:

> 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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