[Trilinos-Users] Trilinos Compilation Error on Linux
Sai P Uppati
uppatis at utexas.edu
Mon Jun 6 18:10:24 EDT 2016
I built my own version of OpenMPI 1.10.2 with CXX=icpc in the
configuration, and even using that, I'm still getting the same compilation
error regarding the //.
Sai
On Mon, Jun 6, 2016 at 1:59 PM, Heroux, Michael A <maherou at sandia.gov>
wrote:
> You can override the default definition of the C++ compiler for OpenMPI by
> using the variable OMPI_CXX. See this page for details:
>
>
>
> https://www.open-mpi.org/doc/v1.8/man1/mpicxx.1.php
>
>
>
> Also, building your own installation of OpenMPI is not too hard, if you
> want to go down that path.
>
>
>
> 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 1:43 PM
> *To: *"John T. Foster" <jfoster at austin.utexas.edu>
> *Cc: *Roscoe Bartlett <rabartl at sandia.gov>, Trilinos Users <
> trilinos-users at trilinos.org>
> *Subject: *[EXTERNAL] Re: [Trilinos-Users] Trilinos Compilation Error on
> Linux
>
>
>
> 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
>
>
>
>
>
> *Error! Filename not specified.*ᐧ
>
>
>
>
>
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