[aspect-devel] Problem compiling Aspect on Tacc-Stampede2

FELIPE ORELLANA ROVIROSA f_orellana at berkeley.edu
Wed May 2 13:19:30 PDT 2018


 Hello Timo,

       The cluster resumed availability.

       I just proceeded compiling,

 it actually finds dealii

   Found deal.II version 9.0.0-pre at
'/home1/apps/intel17/impi17_0/dealii/git20170615/lib/cmake/deal.II'

but it crashes:

   catastrophic error: cannot open source file
"deal.II/lac/trilinos_block_vector.h"
  #  include <deal.II/lac/trilinos_block_vector.h>


This is the whole log:

c506-021[skx](272)$ make release -j32
Scanning dependencies of target release
Switch CMAKE_BUILD_TYPE to Release
-- ====================================================
-- ============ Configuring ASPECT ====================
-- ====================================================
-- Found deal.II version 9.0.0-pre at
'/home1/apps/intel17/impi17_0/dealii/git20170615/lib/cmake/deal.II'
-- Using ASPECT_USE_PETSC = 'OFF'
-- Added 1 tests.
-- Enabling dynamic loading of plugins from the input file
-- Enabling checking of compatible deal.II library when loading plugins
-- Autopilot invoked
-- Run   $ make info  to print a detailed help message
-- Writing config into detailed.log...
-- Configuring done
-- Generating done
-- Build files have been written to: /home1/04020/unfelipe/aspect-1.5/build
gmake[4]: warning: jobserver unavailable: using -j1.  Add `+' to parent
make rule.
Scanning dependencies of target aspect
[  0%] Building CXX object
CMakeFiles/aspect.dir/source/adiabatic_conditions/ascii_data.cc.o
In file included from
/home1/04020/unfelipe/aspect-1.5/source/adiabatic_conditions/ascii_data.cc(22):
/home1/04020/unfelipe/aspect-1.5/include/aspect/global.h(30): catastrophic
error: cannot open source file "deal.II/lac/trilinos_block_vector.h"
  #  include <deal.II/lac/trilinos_block_vector.h>
                                                  ^

compilation aborted for
/home1/04020/unfelipe/aspect-1.5/source/adiabatic_conditions/ascii_data.cc
(code 4)
gmake[6]: ***
[CMakeFiles/aspect.dir/source/adiabatic_conditions/ascii_data.cc.o] Error 4
gmake[5]: *** [CMakeFiles/aspect.dir/all] Error 2
gmake[4]: *** [all] Error 2
make[3]: *** [CMakeFiles/release] Error 2
make[2]: *** [CMakeFiles/release.dir/all] Error 2
make[1]: *** [CMakeFiles/release.dir/rule] Error 2
make: *** [release] Error 2


what should I do?

cheers,
Felipe

On Wed, May 2, 2018 at 12:29 PM, FELIPE ORELLANA ROVIROSA <
f_orellana at berkeley.edu> wrote:

>
>  Hallo Timo,
>
>   Thanks a lot for replying.
>
>    I am going step by step.
>
>   I deleted the build folder, to rebuild everything again.
>
>   I created a new build directory, went into it, and typed:
>
>   cmake -D DEAL_II_DIR=$TACC_DEALII_DIR ..
>
> it seems to have worked:
>
>  login2.stampede2(303)$ cmake -D DEAL_II_DIR=$TACC_DEALII_DIR ..
> -- ====================================================
> -- ============ Configuring ASPECT ====================
> -- ====================================================
> -- Found deal.II version 9.0.0-pre at '/home1/apps/intel17/impi17_0/
> dealii/git20170615/lib/cmake/deal.II'
> -- Using ASPECT_USE_PETSC = 'OFF'
> -- The C compiler identification is Intel 17.0.4.20170411
> -- The CXX compiler identification is Intel 17.0.4.20170411
> -- Check for working C compiler: /opt/intel/compilers_and_
> libraries_2017.4.196/linux/mpi/intel64/bin/mpicc
> -- Check for working C compiler: /opt/intel/compilers_and_
> libraries_2017.4.196/linux/mpi/intel64/bin/mpicc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Check for working CXX compiler: /opt/intel/compilers_and_
> libraries_2017.4.196/linux/mpi/intel64/bin/mpicxx
> -- Check for working CXX compiler: /opt/intel/compilers_and_
> libraries_2017.4.196/linux/mpi/intel64/bin/mpicxx -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Found Perl: /bin/perl (found version "5.16.3")
> -- Added 1 tests.
> -- Performing Test HAVE_DLOPEN
> -- Performing Test HAVE_DLOPEN - Success
> -- Enabling dynamic loading of plugins from the input file
> -- Looking for include file link.h
> -- Looking for include file link.h - found
> -- Enabling checking of compatible deal.II library when loading plugins
> -- Autopilot invoked
> ###
> #
> #  Project  aspect  set up with  deal.II-9.0.0-pre  found at
> #      /home1/apps/intel17/impi17_0/dealii/git20170615
> #
> #  CMAKE_BUILD_TYPE:          Debug
> #
> #  You can now run
> #       $ make                - to compile and link the program
> #       $ make run            - to (compile, link and) run the program
> #
> #       $ make debug          - to switch the build type to 'Debug'
> #       $ make release        - to switch the build type to 'Release'
> #
> #       $ make edit_cache     - to change (cached) configuration variables
> #                               and rerun the configure and generate
> phases of CMake
> #
> #       $ make strip_comments - to strip the source files in this
> #                               directory off the documentation comments
> #       $ make clean          - to remove the generated executable as well
> as
> #                               all intermediate compilation files
> #       $ make runclean       - to remove all output generated by the
> program
> #       $ make distclean      - to clean the directory from _all_ generated
> #                               files (includes clean, runclean and the
> removal
> #                               of the generated build system)
> #       $ make info           - to view this message again
> #
> #  Have a nice day!
> #
> ###
> -- Performing Test HAVE_FP_EXCEPTIONS
> -- Performing Test HAVE_FP_EXCEPTIONS - Failed
> -- No support for feenableexcept(), disabling runtime floating point
> exception checks.
> -- Writing config into detailed.log...
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home1/04020/unfelipe/aspect-
> 1.5/build
> login2.stampede2(304)$
>
> I will proceed with compiling, the optimized version (make release)
>
> Felipe
>
>
> On Wed, May 2, 2018 at 12:09 PM, Timo Heister <heister at clemson.edu> wrote:
>
>> How are you configuring ASPECT? It should be something like
>>
>> cmake -D DEAL_II_DIR=$TACC_DEALII_DIR /your/path/to/your/aspect/sourcedir
>>
>> Can you post your detailed.log from the ASPECT build directory?
>>
>> I am also not sure who built "11) dealii/git20170615" and whether it
>> will work for you.
>>
>> Lastly,
>>
>> > /home1/apps/gcc7_1/impi17_0/dealii/git20170615/include/deal.II/base/utilities.h(28):
>> catastrophic error: cannot open source file "Epetra_Comm.h"
>>
>> This looks like some include paths are missing?!
>>
>>
>>
>>
>> On Wed, May 2, 2018 at 1:49 PM, FELIPE ORELLANA ROVIROSA
>> <f_orellana at berkeley.edu> wrote:
>> >
>> >  Hi all,
>> >
>> >     I am trying to install ASPECT on TACC Stampede2.
>> >
>> >     I have modified my bashrc file so I can use the modules that are
>> already
>> > there installed, so I check the following:
>> >
>> >    login2.stampede2(282)$ module list
>> >
>> > Currently Loaded Modules:
>> >   1) autotools/1.1   4) git/2.9.0      7) impi/17.0.3       10)
>> p4est/2.0
>> >   2) xalt/1.7.7      5) cmake/3.10.2   8) python/2.7.13     11)
>> > dealii/git20170615
>> >   3) TACC            6) intel/17.0.4   9) trilinos/12.10.1
>> >
>> > Inactive Modules:
>> >   1) mkl
>> >
>> >
>> >   Then, I have tried installing two versions of ASPECT (2.0.0-pre and
>> 1.5)
>> > with no success.
>> >   The generating succeeds, it produces the dependencies, etc.
>> >
>> >   But, the problem arises at the moment of compilation. It seemingly
>> fails
>> > when trying to use dealii or trilinos libraries. I am pasting a
>> fraction of
>> > the error message at the end.
>> >
>> >  A guy on Stampede tech support wrote me these messages:
>> > #######################
>> > ''
>> >  When you build ASPECT you have to tell it where trilinos is. I have no
>> > experience with aspect so I don't know whether this is done with a cmake
>> > option, a configure option, or by editing a make include file.
>> >
>> > You need to tell cmake that
>> >
>> > $TACC_DEALII_DIR/include
>> >
>> > is a valid include path
>> > ''########################
>> >
>> >    So, where and how and at what stage should I indicate ASPECT that I
>> am
>> > using the local libraries?
>> >
>> > warm regards,
>> > Felipe
>> >
>> > error message when i compile Aspect 1.5:
>> >
>> > make[2]: *** [CMakeFiles/aspect.dir/source/geometry_model/chunk.cc.o]
>> Error
>> > 4
>> > In file included from
>> > /home1/04020/unfelipe/aspect-1.5/include/aspect/simulator_access.h(32),
>> >                  from
>> > /home1/04020/unfelipe/aspect-1.5/include/aspect/boundary_tem
>> perature/initial_temperature.h(26),
>> >                  from
>> > /home1/04020/unfelipe/aspect-1.5/source/boundary_temperature
>> /initial_temperature.cc(22):
>> > /home1/04020/unfelipe/aspect-1.5/include/aspect/global.h(30):
>> catastrophic
>> > error: cannot open source file "deal.II/lac/trilinos_block_vector.h"
>> >   #  include <deal.II/lac/trilinos_block_vector.h>
>> >
>> >
>> > error message when i compile Aspect 2.0.0-pre:
>> >
>> >   compilation aborted for
>> > /home1/04020/unfelipe/aspect/source/boundary_velocity/interface.cc
>> (code 4)
>> > make[2]: ***
>> > [CMakeFiles/aspect.dir/source/boundary_traction/initial_lith
>> ostatic_pressure.cc.o]
>> > Error 4
>> > In file included from
>> > /home1/apps/gcc7_1/impi17_0/dealii/git20170615/include/deal.
>> II/base/index_set.h(20),
>> >                  from
>> > /home1/apps/gcc7_1/impi17_0/dealii/git20170615/include/deal.
>> II/lac/trilinos_vector.h(24),
>> >                  from
>> > /home1/apps/gcc7_1/impi17_0/dealii/git20170615/include/deal.
>> II/lac/trilinos_parallel_block_vector.h(24),
>> >                  from
>> > /home1/04020/unfelipe/aspect/include/aspect/global.h(34),
>> >                  from
>> > /home1/04020/unfelipe/aspect/include/aspect/plugins.h(25),
>> >                  from
>> > /home1/04020/unfelipe/aspect/include/aspect/boundary_tractio
>> n/interface.h(25),
>> >                  from
>> > /home1/04020/unfelipe/aspect/include/aspect/boundary_tractio
>> n/function.h(25),
>> >                  from
>> > /home1/04020/unfelipe/aspect/source/boundary_traction/function.cc(22):
>> > /home1/apps/gcc7_1/impi17_0/dealii/git20170615/include/deal.
>> II/base/utilities.h(28):
>> > catastrophic error: cannot open source file "Epetra_Comm.h"
>> >   #  include <Epetra_Comm.h>
>> >
>> >
>> > _______________________________________________
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>> > Aspect-devel at geodynamics.org
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>>
>>
>>
>> --
>> Timo Heister
>> http://www.math.clemson.edu/~heister/
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
>
>
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