[Trilinos-Users] Trilinos Compilation Error on Linux
Sai P Uppati
uppatis at utexas.edu
Mon Jun 6 14:29:13 EDT 2016
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
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>>>>
>>>>
>>>
>>
>> _______________________________________________
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>>
>>
>
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