Re: [deal.II] Re: cmake fails when -DDEAL_II_WITH_MPI=ON

[Matthias Maier]

Hi,

On Wed, Jan 24, 2018, at 11:17 CST, Eldar Khattatov  
wrote:

> I forgot to mention, I tried both the development and 8.5.1versions of 
> deal.II and the errors are the same.

The test in question tries to compile a very minimalistic

  int main () { return 0; }

with the given compiler, link interface and linker options.

Have a look at /CMakeFiles/CMakeErrors.log the detailed
compiler output of what exactly fails should be at the very bottom.

I am curious what is going wrong.

Best,
Matthias

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Re: [deal.II] Re: Problem with the use of FE_Nedelec with a mesh file generated from Gmsh

[Jianan Zhang]

Hi, Bruno, 

Just want to inform you and the dealii users who may be interested that my 
problem is solved perfectly by using Ross' new implementation FE_NedelecSZ. 
The results given by brick elements and hexes are quite similar. Thanks a 
lot for the help.

Best
Jianan 

在 2017年12月28日星期四 UTC-5上午10:58:43，Bruno Turcksin写道：
>
> Jianan
>
> 2017-12-28 10:40 GMT-05:00 Jianan Zhang 
> >:
>>
>> So, can you help me contact the people working on the PR to try this out 
>> to see if my code works with the new implementation?
>>
> If you just want to try the new implementation you can take Ross' branch 
>  and see if it works. 
> What would be useful though is to create a test similar to this one 
> 
>  
> but with a failing geometry. This way we can make sure that 1) it works 
> without having to compile all of your code 2) it keeps working in the 
> future by adding the test in our test suite.
>
> Best,
>
> Bruno
>

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[deal.II] Re: PetSc Hybrid MPI-OPENMP Parallelization with Spack Dealii

[Denis Davydov]

Hi,

On Wednesday, January 24, 2018 at 9:13:06 PM UTC+1, Sukhminder Singh wrote:
>
> I installed Spack package of Dealii on a machine with 32 cores (48 virtual 
> cores) and ran a petsc-parallel code. If I run using only one MPI process, 
> then I only get one core running for the solver part. Shouldn't it use all 
> the available cores within a node?  I think its installed with MPI only 
> support, right? Can I use hybrid MPI-OPENMPI parallelization with PetSc  
>
installed using Spack?
>

if you use PETSc, that's how it works, AFAIK PETSc does not support any 
hybrid parallelism.

Elsewhere, deal.II uses TBB (for example in assembly, see other tutorials), 
the number of threads is controlled via 
https://www.dealii.org/developer/doxygen/deal.II/classUtilities_1_1MPI_1_1MPI__InitFinalize.html
 

p.s. it has nothing to do with Spack, which is a package manager to help 
install things consistently. 

Regards,
Denis. 

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[deal.II] Neighbors search within a particular radius of an element

[Sukhminder Singh]

Is there any way to find element neighbors with in a particular *radius* 
from its center? One approach is to compare distance with every other 
element in the whole mesh but then the algorithmic complexity will be 
O(N^2). Another approach is to map all the elements to a coarse structured 
grid with h=*radius *and assign each element a cell number of this 
structured grid. Then I know what are the neighbors of an element which lie 
in the same cell of the grid and then check the distance only with these 
neighbors (this will have O(N) algorithmic complexity).
Is there any simpler way to find neighbors in Dealii, in MPI parallel 
framework? 

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[deal.II] PetSc Hybrid MPI-OPENMP Parallelization with Spack Dealii

[Sukhminder Singh]

I installed Spack package of Dealii on a machine with 32 cores (48 virtual 
cores) and ran a petsc-parallel code. If I run using only one MPI process, 
then I only get one core running for the solver part. Shouldn't it use all 
the available cores within a node?  I think its installed with MPI only 
support, right? Can I use hybrid MPI-OPENMPI parallelization with PetSc 
installed using Spack?

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[deal.II] Re: cmake fails when -DDEAL_II_WITH_MPI=ON

[Eldar Khattatov]

I forgot to mention, I tried both the development and 8.5.1versions of 
deal.II and the errors are the same.

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[deal.II] cmake fails when -DDEAL_II_WITH_MPI=ON

[Eldar Khattatov]

I was asked to help a fellow graduate student with installing deal.ii on 
his laptop that runs Ubuntu 17.10, and for some reason, I end up having the 
following error message from cmake:

CMake Error at cmake/setup_finalize.cmake:95 (MESSAGE):
>
>   
>
> Configuration error: Cannot compile a test program with the final set 
>> of
>
> compiler and linker flags:
>
>   CXX flags (DEBUG): -pedantic -fPIC -Wall -Wextra -Wpointer-arith 
>> -Wwrite-strings -Wsynth -Wsign-compare -Wswitch -Woverloaded-virtual 
>> -Wno-placement-new -Wno-deprecated-declarations -Wno-literal-suffix 
>> -fopenmp-simd -std=c++17 -Wno-parentheses -Wno-unused-local-typedefs -Og 
>> -ggdb -Wa,--compress-debug-sections
>
>   LD flags  (DEBUG): -Wl,--as-needed -rdynamic -fuse-ld=gold -pthread 
>> -ggdb
>
>   LIBRARIES (DEBUG): 
>> /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_usempif08.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_usempi_ignore_tkr.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_mpifh.so;dl;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/libamd.so;rt;/usr/lib/x86_64-linux-gnu/libparpack.so;/usr/lib/x86_64-linux-gnu/libarpack.so;/usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so;gfortran;quadmath;m;c;gcc_s;gcc;/usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libboost_iostreams.so;/usr/lib/x86_64-linux-gnu/libboost_serialization.so;/usr/lib/x86_64-linux-gnu/libboost_system.so;/usr/lib/x86_64-linux-gnu/libboost_thread.so;/usr/lib/x86_64-linux-gnu/libboost_regex.so;/usr/lib/x86_64-linux-gnu/libboost_chrono.so;/usr/lib/x86_64-linux-gnu/libboost_date_time.so;/usr/lib/x86_64-linux-gnu/libboost_atomic.so;pthread;/usr/lib/x86_64-linux-gnu/libnetcdf_c++.so;/usr/lib/x86_64-linux-gnu/libnetcdf.so;
>
> 
>
> Call Stack (most recent call first):
>
>   cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
>
>   CMakeLists.txt:132 (VERBOSE_INCLUDE)
>
>
>> -- Configuring incomplete, errors occurred!
>
> See also 
>> "/home/username/Downloads/dealii/build/CMakeFiles/CMakeOutput.log".
>
> See also "/home/username/Downloads/dealii/build/CMakeFiles/CMakeError.log".
>
>
When configured without MPI everything works smoothly. The openmpi version 
3.1 is installed, and it works fine on its own.
As I have never faced this issue before, could you please help me with 
figuring out what is going on?

I have also attached the complete console output of the cmake command. 

Thank you!

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Surface-Pro-4:~/Downloads/dealii/build$ cmake 
-DDEAL_INSTALL_PREFIX=~/libs/dealii -DDEAL_II_WITH_MPI=ON  ../
-- This is CMake 3.9.1
-- 
-- Include /home/username/Downloads/dealii/cmake/setup_external_macros.cmake
-- Include /home/username/Downloads/dealii/cmake/macros/macro_add_flags.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_check_compiler_setup.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_check_cxx_compiler_bug.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_check_mpi_interface.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_clear_cmake_required.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_configure_feature.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_deal_ii_add_definitions.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_deal_ii_add_library.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_deal_ii_add_test.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_deal_ii_find_file.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_deal_ii_find_library.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_deal_ii_find_path.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_deal_ii_find_program.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_deal_ii_initialize_cached_variables.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_deal_ii_insource_setup_target.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_deal_ii_invoke_autopilot.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_deal_ii_package_handle.cmake
-- Include 
/home/username/Downloads/dealii/cmake/macros/macro_deal_ii_pickup

Re: [deal.II] Re: installation error

[Juan Carlos Araujo Cabarcas]

Please find the file: detailed.log attached.

El martes, 23 de enero de 2018, 17:02:14 (UTC-5), Wolfgang Bangerth 
escribió:
>
> On 01/23/2018 02:13 PM, Bruno Turcksin wrote: 
> > 
> > mypath/dealii/source/lac/scalapack.cc:243:91: error: there are no 
> > arguments to ‘MPI_Comm_create_group’ that depend on a template 
> parameter, 
> > so a declaration of ‘MPI_Comm_create_group’ must be available 
> [-fpermissive] 
> > ierr = MPI_Comm_create_group(MPI_COMM_WORLD, group_union, 5, 
> > &mpi_communicator_union); 
> > 
> > Do you need scalapack? If you don't, just add DEAL_II_WITH_SCALAPACK=OFF 
>
> Out of curiosity, can you also send the output of the detailed.log file in 
> your build directory? 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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###
#
#  deal.II configuration:
#CMAKE_BUILD_TYPE:   DebugRelease
#BUILD_SHARED_LIBS:  ON
#CMAKE_INSTALL_PREFIX:   /home/ju4nk4/Soft/dealii
#CMAKE_SOURCE_DIR:   /home/ju4nk4/Soft/dealii
#(version 9.0.0-pre, shortrev 55c9e45)
#CMAKE_BINARY_DIR:   /home/ju4nk4/Soft/dealii/build
#CMAKE_CXX_COMPILER: GNU 4.8.4 on platform Linux x86_64
#/usr/bin/c++
#CMAKE_C_COMPILER:   /usr/bin/cc
#CMAKE_Fortran_COMPILER: /usr/bin/gfortran
#CMAKE_GENERATOR:Unix Makefiles
#
#  Base configuration (prior to feature configuration):
#DEAL_II_CXX_FLAGS:-pedantic -fPIC -Wall -Wextra 
-Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Wswitch 
-Woverloaded-virtual -Wno-deprecated-declarations -Wno-literal-suffix -std=c++11
#DEAL_II_CXX_FLAGS_RELEASE:-O2 -funroll-loops -funroll-all-loops 
-fstrict-aliasing -Wno-unused-local-typedefs
#DEAL_II_CXX_FLAGS_DEBUG:  -Og -ggdb -Wa,--compress-debug-sections
#DEAL_II_LINKER_FLAGS: -Wl,--as-needed -rdynamic -fuse-ld=gold
#DEAL_II_LINKER_FLAGS_RELEASE: 
#DEAL_II_LINKER_FLAGS_DEBUG:   -ggdb
#DEAL_II_DEFINITIONS:  
#DEAL_II_DEFINITIONS_RELEASE:  
#DEAL_II_DEFINITIONS_DEBUG:DEBUG
#DEAL_II_USER_DEFINITIONS: 
#DEAL_II_USER_DEFINITIONS_REL: 
#DEAL_II_USER_DEFINITIONS_DEB: DEBUG
#DEAL_II_INCLUDE_DIRS  
#DEAL_II_USER_INCLUDE_DIRS:
#DEAL_II_BUNDLED_INCLUDE_DIRS: 
#DEAL_II_LIBRARIES:m
#DEAL_II_LIBRARIES_RELEASE:
#DEAL_II_LIBRARIES_DEBUG:  
#
#  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION 
= ON):
#  ( DEAL_II_WITH_64BIT_INDICES = OFF )
#  ( DEAL_II_WITH_ADOLC = OFF )
#DEAL_II_WITH_ARPACK set up with external dependencies
#ARPACK_LINKER_FLAGS = 
#ARPACK_LIBRARIES = 
/usr/lib/libarpack.so;/usr/lib/liblapack.so;/usr/lib/libblas.so;gfortran;quadmath;m;c;/usr/lib/openmpi/lib/libmpi.so;dl;/usr/lib/x86_64-linux-gnu/libhwloc.so
#  ( DEAL_II_WITH_ASSIMP = OFF )
#DEAL_II_WITH_BOOST set up with bundled packages
#BOOST_CXX_FLAGS = -Wno-unused-local-typedefs
#BOOST_BUNDLED_INCLUDE_DIRS = 
/home/ju4nk4/Soft/dealii/bundled/boost-1.62.0/include
#BOOST_LIBRARIES = rt
#  ( DEAL_II_WITH_CUDA = OFF )
#  ( DEAL_II_WITH_CXX14 = OFF )
#  ( DEAL_II_WITH_CXX17 = OFF )
#DEAL_II_WITH_GMSH set up with external dependencies
#GMSH_EXE = /usr/bin/gmsh
#  ( DEAL_II_WITH_GSL = OFF )
#  ( DEAL_II_WITH_HDF5 = OFF )
#DEAL_II_WITH_LAPACK set up with external dependencies
#LAPACK_WITH_64BIT_BLAS_INDICES = OFF
#LAPACK_LINKER_FLAGS = 
#LAPACK_LIBRARIES = 
/usr/lib/liblapack.so;/usr/lib/libblas.so;gfortran;quadmath;m;c
#DEAL_II_WITH_METIS set up with external dependencies
#METIS_VERSION = 5.1.0
#METIS_DIR = /home/ju4nk4/Soft/metis-5.1.0
#METIS_INCLUDE_DIRS = /home/ju4nk4/Soft/metis-5.1.0/include
#METIS_USER_INCLUDE_DIRS = /home/ju4nk4/Soft/metis-5.1.0/include
#METIS_LIBRARIES = 
/home/ju4nk4/Soft/metis-5.1.0/build/Linux-x86_64/libmetis/libmetis.a;/usr/lib/openmpi/lib/libmpi.so;dl;/usr/lib/x86_64-linux-gnu/libhwloc.so
#DEAL_II_WITH_MPI set up with external dependencies
#MPI_V

[deal.II] Difference between Sacado and Adol-C for differentiation

['Maxi Miller' via deal.II User Group]

After both Sacado and Adol-C can be linked into the library (and both can 
serve the same purpose):
What is the difference between both? Why should I prefer one over the other?
Thanks!

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