[aspect-devel] Problem compiling Aspect on Tacc-Stampede2
John Naliboff
jbnaliboff at ucdavis.edu
Wed May 2 14:10:43 PDT 2018
Hi all,
Just a quick bit of clarification - my recommendation is to build on a
"development" SKX node, using the "idev" command.
The SKX nodes give the best scaling performance and compiling on an SKX
development nodes means you are guaranteed to have compiled under the
right architecture (e.g., if you submit a job to an SKX node). You also
of course compile much faster (access to 48 cores) and I believe that
either the deal.II or Trilinos builds on the head nodes may have run
into memory issues.
The command to run an interactive development session on an SKX
development node is:
idev -p skx-dev -N 1 -n 48 -m 90
where skx-dev is the partition, N is the number of nodes, n is the
number tasks and m is the number of minutes.
More information here:
https://portal.tacc.utexas.edu/user-guides/stampede2#running-idev
Felipe - You are following the instructions I sent over, yes? I'm not
sure what's going wrong, but if you can wait until next Monday I'll have
a chance to try recompiling on see if anything has changed since I last
compiled (1-2 months).
Cheers,
John
On 05/02/2018 12:40 PM, FELIPE ORELLANA ROVIROSA wrote:
>
> Hi Timo,
>
> Gotta wait:
>
> The compute nodes on Stampede2 are down at the moment. I am
> asking them about this issue.
>
> As far as I understand it is highly recommended to be
> hanging from compute nodes while carrying out compilation.
>
> thanks,
> Felipe
>
> On Wed, May 2, 2018 at 12:29 PM, FELIPE ORELLANA ROVIROSA
> <f_orellana at berkeley.edu <mailto: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
> <mailto:heister at clemson.edu>> wrote:
>
> How are you configuring ASPECT? It should be something like
>
> cmake -D DEAL_II_DIR=$TACC_DEALII_DIR
> /your/path/to/your/aspect/sourcedir
>
> Can you post your detailed.log from the ASPECT build directory?
>
> I am also not sure who built "11) dealii/git20170615" and
> whether it
> will work for you.
>
> Lastly,
>
> >
> /home1/apps/gcc7_1/impi17_0/dealii/git20170615/include/deal.II/base/utilities.h(28):
> catastrophic error: cannot open source file "Epetra_Comm.h"
>
> This looks like some include paths are missing?!
>
>
>
>
> On Wed, May 2, 2018 at 1:49 PM, FELIPE ORELLANA ROVIROSA
> <f_orellana at berkeley.edu <mailto:f_orellana at berkeley.edu>> wrote:
> >
> > Hi all,
> >
> > I am trying to install ASPECT on TACC Stampede2.
> >
> > I have modified my bashrc file so I can use the modules
> that are already
> > there installed, so I check the following:
> >
> > login2.stampede2(282)$ 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_temperature/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_lithostatic_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_traction/interface.h(25),
> > from
> >
> /home1/04020/unfelipe/aspect/include/aspect/boundary_traction/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
> <mailto:Aspect-devel at geodynamics.org>
> >
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>
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/
> <http://www.math.clemson.edu/%7Eheister/>
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