[aspect-devel] Problem compiling Aspect on Tacc-Stampede2
FELIPE ORELLANA ROVIROSA
f_orellana at berkeley.edu
Wed May 2 13:23:28 PDT 2018
Hello,
Some more info that could be useful:
This is the detailed.log file:
###
#
# ASPECT configuration:
# ASPECT_VERSION: 1.5.0
# DEAL_II_DIR:
/home1/apps/intel17/impi17_0/dealii/git20170615/lib/cmake/deal.II
# DEAL_II VERSION: 9.0.0-pre
# ASPECT_USE_PETSC: OFF
# ASPECT_USE_FP_EXCEPTIONS: OFF
# ASPECT_RUN_ALL_TESTS: OFF
# ASPECT_USE_SHARED_LIBS: ON
# ASPECT_HAVE_LINK_H: ON
# CMAKE_BUILD_TYPE: Release
# CMAKE_INSTALL_PREFIX: /usr/local
# CMAKE_SOURCE_DIR: /home1/04020/unfelipe/aspect-1.5
# CMAKE_BINARY_DIR: /home1/04020/unfelipe/aspect-1.5/build
# CMAKE_CXX_COMPILER: Intel 17.0.4.20170411 on platform Linux
x86_64
#
/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpicxx
# CMAKE_C_COMPILER:
/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpicc
#
# LINKAGE: DYNAMIC
#
###
~
Felipe
On Wed, May 2, 2018 at 1:19 PM, FELIPE ORELLANA ROVIROSA <
f_orellana at berkeley.edu> wrote:
>
> 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_libra
>> ries_2017.4.196/linux/mpi/intel64/bin/mpicc
>> -- Check for working C compiler: /opt/intel/compilers_and_libra
>> ries_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_libra
>> ries_2017.4.196/linux/mpi/intel64/bin/mpicxx
>> -- Check for working CXX compiler: /opt/intel/compilers_and_libra
>> ries_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=$TACC_DEALII_DIR /your/path/to/your/aspect/sour
>>> cedir
>>>
>>> Can you post your detailed.log from the ASPECT build directory?
>>>
>>> I am also not sure who built "11) dealii/git20170615" and whether it
>>> will work for you.
>>>
>>> Lastly,
>>>
>>> > /home1/apps/gcc7_1/impi17_0/dealii/git20170615/include/deal.II/base/utilities.h(28):
>>> catastrophic error: cannot open source file "Epetra_Comm.h"
>>>
>>> This looks like some include paths are missing?!
>>>
>>>
>>>
>>>
>>> On Wed, May 2, 2018 at 1:49 PM, FELIPE ORELLANA ROVIROSA
>>> <f_orellana at berkeley.edu> wrote:
>>> >
>>> > Hi all,
>>> >
>>> > I am trying to install ASPECT on TACC Stampede2.
>>> >
>>> > I have modified my bashrc file so I can use the modules that are
>>> already
>>> > there installed, so I check the following:
>>> >
>>> > login2.stampede2(282)$ 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_ac
>>> cess.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>
>>> >
>>> >
>>> > _______________________________________________
>>> > Aspect-devel mailing list
>>> > Aspect-devel at geodynamics.org
>>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ge
>>> odynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=Dw
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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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