Re: [deal.II] CellDataStorage with mesh refinement

['Frederik S.' via deal.II User Group]

Hello Timo!

Sorry it took so long, I was on a conference this week and didn't come to 
answer.
Many thanks for the example! I read through all the documentation pages, 
but it didn't come to my mind to just check the source code of this 
classes... Thanks again, this will help me a lot!

PS: see also my answer to Jean-Pauls message.

Am Mittwoch, 1. November 2017 21:17:57 UTC+1 schrieb Timo Heister:
>
> > I tried to use the class, but I still have some Problems. In the example 
> you 
> > are just transferring an integer variable. Is it also possible to 
> transfer a 
> > whole CellDataStorage element (or at least some packed vector with ist 
> > elements) from a parent cell to each child? Do you also have an example 
> how 
> > this works? 
>
> You can transfer whatever you want and the "status" argument will tell 
> you if you have to convert your data to children or parents. 
>
> Examples? It is used in SolutionTransfer and 
> ContinuousQuadratureDataTransfer: 
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dealii_dealii_blob_60bfd3170a465002ac1404dc36a5ba9671254b71_source_distributed_solution-5Ftransfer.cc-23L84=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=4DhDywRdwgpQcqLQhc9e3vXnNh9twLFXh6cAv-rYOtU=HDE5UAeI6pVJZbKAVdMR4mt-Hb-RJxrDcUsUjCX4myo=
>  
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dealii_dealii_blob_a0073ac1c0e88a30702a52f6522cbfffe1834ed1_include_deal.II_base_quadrature-5Fpoint-5Fdata.h-23L735=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=4DhDywRdwgpQcqLQhc9e3vXnNh9twLFXh6cAv-rYOtU=j5xv1X624c05TmUCkWaj5qBdYefoSr6JBbEZ1-PIhcU=
>  
>
> We also use it in ASPECT to transfer particles: 
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_geodynamics_aspect_blob_0eec247edd99cd782a8fc66b36b140ce7a4105ae_source_particle_particle-5Fhandler.cc-23L858=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=4DhDywRdwgpQcqLQhc9e3vXnNh9twLFXh6cAv-rYOtU=OmRYoVuKEIL1dlaaCOgQLqNoCmHaHzJulO4dsMuAq2o=
>  
>
> -- 
> Timo Heister 
> http://www.math.clemson.edu/~heister/ 
>

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Re: [deal.II] CellDataStorage with mesh refinement

['Frederik S.' via deal.II User Group]

Sorry it took so long, I was on a conference this week and didn't come to 
answer.

Many thanks for the example! I read through all the documentation pages, 
but it didn't come to my mind to just check the source code of this 
classes... Thanks again, this will help me a lot!

PS: see also my answer to Jean-Pauls message.

Am Mittwoch, 1. November 2017 21:17:57 UTC+1 schrieb Timo Heister:
>
> > I tried to use the class, but I still have some Problems. In the example 
> you 
> > are just transferring an integer variable. Is it also possible to 
> transfer a 
> > whole CellDataStorage element (or at least some packed vector with ist 
> > elements) from a parent cell to each child? Do you also have an example 
> how 
> > this works? 
>
> You can transfer whatever you want and the "status" argument will tell 
> you if you have to convert your data to children or parents. 
>
> Examples? It is used in SolutionTransfer and 
> ContinuousQuadratureDataTransfer: 
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dealii_dealii_blob_60bfd3170a465002ac1404dc36a5ba9671254b71_source_distributed_solution-5Ftransfer.cc-23L84=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=4DhDywRdwgpQcqLQhc9e3vXnNh9twLFXh6cAv-rYOtU=HDE5UAeI6pVJZbKAVdMR4mt-Hb-RJxrDcUsUjCX4myo=
>  
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dealii_dealii_blob_a0073ac1c0e88a30702a52f6522cbfffe1834ed1_include_deal.II_base_quadrature-5Fpoint-5Fdata.h-23L735=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=4DhDywRdwgpQcqLQhc9e3vXnNh9twLFXh6cAv-rYOtU=j5xv1X624c05TmUCkWaj5qBdYefoSr6JBbEZ1-PIhcU=
>  
>
> We also use it in ASPECT to transfer particles: 
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_geodynamics_aspect_blob_0eec247edd99cd782a8fc66b36b140ce7a4105ae_source_particle_particle-5Fhandler.cc-23L858=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=4DhDywRdwgpQcqLQhc9e3vXnNh9twLFXh6cAv-rYOtU=OmRYoVuKEIL1dlaaCOgQLqNoCmHaHzJulO4dsMuAq2o=
>  
>
> -- 
> Timo Heister 
> http://www.math.clemson.edu/~heister/ 
>

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Re: [deal.II] New Mac OSX brew package

[Denis Davydov]

> On 9 Nov 2017, at 23:12, luca.heltai  wrote:
> 
> It does not compile, anyway…
> 
> :D 
> 
> Maybe Denis can help: I get the following when trying to compile pkg-config 
> using gcc installed with spack:

a lot of things break on macOS when compiling with GCC. 
For example CMake was a problem on Sierra 
https://github.com/spack/spack/issues/1847 
 

One can work-around such issue by either using system-provided tools or 
building some of those with Clang and the rest with GCC,
but frankly I don’t see a reason doing it on macOS. There’s more pain than gain.

Also compiler errors with templates are much better with Clang, so I kinda like 
it more ;-)

Cheers,
Denis.

> 
> In file included from 
> /System/Library/Frameworks/Security.framework/Headers/AuthSession.h:32:0,
> from 
> /System/Library/Frameworks/Security.framework/Headers/Security.h:43,
> from 
> /System/Library/Frameworks/CoreServices.framework/Frameworks/OSServices.framework/Headers/CSIdentity.h:43,
> from 
> /System/Library/Frameworks/CoreServices.framework/Frameworks/OSServices.framework/Headers/OSServices.h:27,
> from 
> /System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Headers/IconsCore.h:23,
> from 
> /System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Headers/LaunchServices.h:22,
> from 
> /System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:39,
> from gunicollate.c:30:
> /System/Library/Frameworks/Security.framework/Headers/Authorization.h:193:7: 
> error: variably modified ‘bytes’ at file scope
>  char bytes[kAuthorizationExternalFormLength];
>   ^
> make[6]: *** [libglib_2_0_la-gunicollate.lo] Error 1
> make[5]: *** [all-recursive] Error 1
> make[4]: *** [all] Error 2
> make[3]: *** [all-recursive] Error 1
> make[2]: *** [all] Error 2
> make[1]: *** [all-recursive] Error 1
> make: *** [all] Error 2
> 
> L.
> 
>> On 9 Nov 2017, at 23:09, Timo Heister  wrote:
>> 
>>> I'm using clang+gfortran. I have not tried using gcc for everything, but I 
>>> could give it a shot if you think it would be worth it.
>> 
>> No, I was just curious. I don't have a strong preference for either.
>> 
>> -- 
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see 
>> https://groups.google.com/d/forum/dealii?hl=en
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> 
> -- 
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Re: [deal.II] New Mac OSX brew package

[luca.heltai]

It does not compile, anyway…

:D 

Maybe Denis can help: I get the following when trying to compile pkg-config 
using gcc installed with spack:

In file included from 
/System/Library/Frameworks/Security.framework/Headers/AuthSession.h:32:0,
 from 
/System/Library/Frameworks/Security.framework/Headers/Security.h:43,
 from 
/System/Library/Frameworks/CoreServices.framework/Frameworks/OSServices.framework/Headers/CSIdentity.h:43,
 from 
/System/Library/Frameworks/CoreServices.framework/Frameworks/OSServices.framework/Headers/OSServices.h:27,
 from 
/System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Headers/IconsCore.h:23,
 from 
/System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Headers/LaunchServices.h:22,
 from 
/System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:39,
 from gunicollate.c:30:
/System/Library/Frameworks/Security.framework/Headers/Authorization.h:193:7: 
error: variably modified ‘bytes’ at file scope
  char bytes[kAuthorizationExternalFormLength];
   ^
make[6]: *** [libglib_2_0_la-gunicollate.lo] Error 1
make[5]: *** [all-recursive] Error 1
make[4]: *** [all] Error 2
make[3]: *** [all-recursive] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

L.

> On 9 Nov 2017, at 23:09, Timo Heister  wrote:
> 
>> I'm using clang+gfortran. I have not tried using gcc for everything, but I 
>> could give it a shot if you think it would be worth it.
> 
> No, I was just curious. I don't have a strong preference for either.
> 
> -- 
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see 
> https://groups.google.com/d/forum/dealii?hl=en
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Re: [deal.II] New Mac OSX brew package

[Timo Heister]

> I'm using clang+gfortran. I have not tried using gcc for everything, but I 
> could give it a shot if you think it would be worth it.

No, I was just curious. I don't have a strong preference for either.

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Re: [deal.II] Re: New Mac OSX brew package

[luca.heltai]

Oh, and naturally ’s/brew/spack/g’ in my previous email.


clang --version
Apple LLVM version 9.0.0 (clang-900.0.38)
Target: x86_64-apple-darwin17.0.0
Thread model: posix
InstalledDir: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

and 

gfortran --version
GNU Fortran (GCC) 7.2.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
/Applications/deal.II-9.0-spack.app/Contents/Resources/spack/opt/spack/darwin-highsierra-x86_64/clang-9.0.0-apple/gcc-7.2.0-zjkdy42fjmlapty3f7khykdwz4366mwt/bin/gfortran


> On 9 Nov 2017, at 19:21, Denis Davydov  wrote:
> 
> nice!
> 
> @Timo: If I am not mistaken, it's Apple's Clang 9.0.0 + gfortran 7.2.0.  
> 
> On Thursday, November 9, 2017 at 9:41:52 AM UTC+1, Luca Heltai wrote:
> Dear All, 
> 
> I just finished uploading a new brew based package for deal.II with a 
> 9.0pre.1 version: 
> 
> https://github.com/luca-heltai/dealii/releases/tag/v9.0.pre.1 
> 
> It was compiled on a Mac OS X High Sierra: 10.13 (17A405), with Xcode 9.0.1 
> (9A1004). 
> 
> The application contains a full `spack` installation at 
> 
> `/Applications/deal.II-9.0-spack/Contents/Resources/spack` 
> 
> You’ll have access to all spack facilities (including modules) by adding 
> 
> . 
> /Applications/deal.II-9.0-spack.app/Contents/Resources/share/deal.II/dealii.conf
>  
> 
> to your ~/.profile file. 
> 
> Summary.log: 
> 
> ### 
> # 
> #  deal.II configuration: 
> #CMAKE_BUILD_TYPE:   DebugRelease 
> #BUILD_SHARED_LIBS:  ON 
> #CMAKE_INSTALL_PREFIX:   
> /Applications/deal.II-9.0-spack.app/Contents/Resources 
> #CMAKE_SOURCE_DIR:   /Users/heltai/dealii/dealii 
> #(version 9.0.0-pre, shortrev 88babf1a4d) 
> #CMAKE_BINARY_DIR:   /Users/heltai/dealii/dealii/build-9.0-spack 
> #CMAKE_CXX_COMPILER: AppleClang 9.0.0.938 on platform Darwin 
> x86_64 
> #
> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/bin/mpic++ 
> # 
> #  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, 
> DEAL_II_ALLOW_AUTODETECTION = ON): 
> #  ( DEAL_II_WITH_64BIT_INDICES = OFF ) 
> #DEAL_II_WITH_ADOLC set up with external dependencies 
> #DEAL_II_WITH_ARPACK set up with external dependencies 
> #DEAL_II_WITH_ASSIMP set up with external dependencies 
> #DEAL_II_WITH_BOOST set up with external dependencies 
> #  ( DEAL_II_WITH_CUDA = OFF ) 
> #DEAL_II_WITH_CXX14 = ON 
> #DEAL_II_WITH_CXX17 = ON 
> #DEAL_II_WITH_GSL set up with external dependencies 
> #DEAL_II_WITH_HDF5 set up with external dependencies 
> #DEAL_II_WITH_LAPACK set up with external dependencies 
> #DEAL_II_WITH_METIS set up with external dependencies 
> #DEAL_II_WITH_MPI set up with external dependencies 
> #DEAL_II_WITH_MUPARSER set up with external dependencies 
> #DEAL_II_WITH_NANOFLANN set up with external dependencies 
> #DEAL_II_WITH_NETCDF set up with external dependencies 
> #DEAL_II_WITH_OPENCASCADE set up with external dependencies 
> #DEAL_II_WITH_P4EST set up with external dependencies 
> #DEAL_II_WITH_PETSC set up with external dependencies 
> #DEAL_II_WITH_SLEPC set up with external dependencies 
> #DEAL_II_WITH_SUNDIALS set up with external dependencies 
> #DEAL_II_WITH_THREADS set up with external dependencies 
> #DEAL_II_WITH_TRILINOS set up with external dependencies 
> #DEAL_II_WITH_UMFPACK set up with external dependencies 
> #DEAL_II_WITH_ZLIB set up with external dependencies 
> # 
> #  Component configuration: 
> #  ( DEAL_II_COMPONENT_DOCUMENTATION = OFF ) 
> #  ( DEAL_II_COMPONENT_EXAMPLES = OFF ) 
> #DEAL_II_COMPONENT_PACKAGE 
> #  ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF ) 
> # 
> #  Detailed information (compiler flags, feature configuration) can be found 
> in detailed.log 
> # 
> #  Run  $ ninja info  to print a help message with a list of top level 
> targets 
> # 
> ### 
> 
> And this is the output of spack find: 
> 
> ==> 74 installed packages. 
> -- darwin-highsierra-x86_64 / clang@9.0.0-apple - 
> adol-c@develop  freetype@2.7.1lcms@2.8 
> nasm@2.11.06pkg-config@0.29.2 
> arpack-ng@3.5.0 gcc@7.2.0 libjpeg-turbo@1.5.0  
> ncurses@6.0 python@2.7.14 
> assimp@4.0.1gdbm@1.13 libpng@1.6.29
> net...@4.4.1.1  readline@7.0 
> astyle@2.04 get...@0.19.8.1  libsigsegv@2.11  
> netcdf-cxx@4.2  slepc@3.8.0 
> autoconf@2.69   ghostscript@9.21  libtiff@4.0.8
> netlib-scalapack@2.0.2  sqlite@3.20.0 
> 

Re: [deal.II] New Mac OSX brew package

[Luca Heltai]

I'm using clang+gfortran. I have not tried using gcc for everything, but I 
could give it a shot if you think it would be worth it. 

Luca

> On 9 Nov 2017, at 17:59, Timo Heister  wrote:
> 
> thanks, Luca!
> 
> Are you using the system clang with the fortran compiler from gcc? Are
> the spack packages compiled with gcc or with clang?
> 
>> On Thu, Nov 9, 2017 at 3:40 AM, luca.heltai  wrote:
>> Dear All,
>> 
>> I just finished uploading a new brew based package for deal.II with a 
>> 9.0pre.1 version:
>> 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_luca-2Dheltai_dealii_releases_tag_v9.0.pre.1=DwIFaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=B4_I7m9Fb7UJr3fQ0YmopMCt2BsnKOY2uoFIQ28VKXs=UQTroVQ4XmKFbV4qTi4pGa6KPdjCdxglDVCGB7IPIo4=
>>  
>> 
>> It was compiled on a Mac OS X High Sierra: 10.13 (17A405), with Xcode 9.0.1 
>> (9A1004).
>> 
>> The application contains a full `spack` installation at
>> 
>> `/Applications/deal.II-9.0-spack/Contents/Resources/spack`
>> 
>> You’ll have access to all spack facilities (including modules) by adding
>> 
>> . 
>> /Applications/deal.II-9.0-spack.app/Contents/Resources/share/deal.II/dealii.conf
>> 
>> to your ~/.profile file.
>> 
>> Summary.log:
>> 
>> ###
>> #
>> #  deal.II configuration:
>> #CMAKE_BUILD_TYPE:   DebugRelease
>> #BUILD_SHARED_LIBS:  ON
>> #CMAKE_INSTALL_PREFIX:   
>> /Applications/deal.II-9.0-spack.app/Contents/Resources
>> #CMAKE_SOURCE_DIR:   /Users/heltai/dealii/dealii
>> #(version 9.0.0-pre, shortrev 88babf1a4d)
>> #CMAKE_BINARY_DIR:   /Users/heltai/dealii/dealii/build-9.0-spack
>> #CMAKE_CXX_COMPILER: AppleClang 9.0.0.938 on platform Darwin 
>> x86_64
>> #
>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/bin/mpic++
>> #
>> #  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, 
>> DEAL_II_ALLOW_AUTODETECTION = ON):
>> #  ( DEAL_II_WITH_64BIT_INDICES = OFF )
>> #DEAL_II_WITH_ADOLC set up with external dependencies
>> #DEAL_II_WITH_ARPACK set up with external dependencies
>> #DEAL_II_WITH_ASSIMP set up with external dependencies
>> #DEAL_II_WITH_BOOST set up with external dependencies
>> #  ( DEAL_II_WITH_CUDA = OFF )
>> #DEAL_II_WITH_CXX14 = ON
>> #DEAL_II_WITH_CXX17 = ON
>> #DEAL_II_WITH_GSL set up with external dependencies
>> #DEAL_II_WITH_HDF5 set up with external dependencies
>> #DEAL_II_WITH_LAPACK set up with external dependencies
>> #DEAL_II_WITH_METIS set up with external dependencies
>> #DEAL_II_WITH_MPI set up with external dependencies
>> #DEAL_II_WITH_MUPARSER set up with external dependencies
>> #DEAL_II_WITH_NANOFLANN set up with external dependencies
>> #DEAL_II_WITH_NETCDF set up with external dependencies
>> #DEAL_II_WITH_OPENCASCADE set up with external dependencies
>> #DEAL_II_WITH_P4EST set up with external dependencies
>> #DEAL_II_WITH_PETSC set up with external dependencies
>> #DEAL_II_WITH_SLEPC set up with external dependencies
>> #DEAL_II_WITH_SUNDIALS set up with external dependencies
>> #DEAL_II_WITH_THREADS set up with external dependencies
>> #DEAL_II_WITH_TRILINOS set up with external dependencies
>> #DEAL_II_WITH_UMFPACK set up with external dependencies
>> #DEAL_II_WITH_ZLIB set up with external dependencies
>> #
>> #  Component configuration:
>> #  ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
>> #  ( DEAL_II_COMPONENT_EXAMPLES = OFF )
>> #DEAL_II_COMPONENT_PACKAGE
>> #  ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
>> #
>> #  Detailed information (compiler flags, feature configuration) can be found 
>> in detailed.log
>> #
>> #  Run  $ ninja info  to print a help message with a list of top level 
>> targets
>> #
>> ###
>> 
>> And this is the output of spack find:
>> 
>> ==> 74 installed packages.
>> -- darwin-highsierra-x86_64 / clang@9.0.0-apple -
>> adol-c@develop  freetype@2.7.1lcms@2.8 
>> nasm@2.11.06pkg-config@0.29.2
>> arpack-ng@3.5.0 gcc@7.2.0 libjpeg-turbo@1.5.0  
>> ncurses@6.0 python@2.7.14
>> assimp@4.0.1gdbm@1.13 libpng@1.6.29
>> netcdf@4.4.1.1  readline@7.0
>> astyle@2.04 gettext@0.19.8.1  libsigsegv@2.11  
>> netcdf-cxx@4.2  slepc@3.8.0
>> autoconf@2.69   ghostscript@9.21  libtiff@4.0.8
>> netlib-scalapack@2.0.2  sqlite@3.20.0
>> automake@1.15.1 glm@0.9.7.1   libtool@2.4.6
>> ninja@1.8.2 suite-sparse@4.5.5
>> bison@3.0.4 gmp@6.1.2 libxml2@2.9.4
>> numdiff@5.9.0   sundials@3.0.0
>> boost@1.63.0   

[deal.II] Re: New Mac OSX brew package

[Denis Davydov]

nice!

@Timo: If I am not mistaken, it's Apple's Clang 9.0.0 + gfortran 7.2.0.  

On Thursday, November 9, 2017 at 9:41:52 AM UTC+1, Luca Heltai wrote:
>
> Dear All, 
>
> I just finished uploading a new brew based package for deal.II with a 
> 9.0pre.1 version: 
>
> https://github.com/luca-heltai/dealii/releases/tag/v9.0.pre.1 
>
> It was compiled on a Mac OS X High Sierra: 10.13 (17A405), with Xcode 
> 9.0.1 (9A1004). 
>
> The application contains a full `spack` installation at 
>
> `/Applications/deal.II-9.0-spack/Contents/Resources/spack` 
>
> You’ll have access to all spack facilities (including modules) by adding 
>
> . 
> /Applications/deal.II-9.0-spack.app/Contents/Resources/share/deal.II/dealii.conf
>  
>
>
> to your ~/.profile file. 
>
> Summary.log: 
>
> ### 
> # 
> #  deal.II configuration: 
> #CMAKE_BUILD_TYPE:   DebugRelease 
> #BUILD_SHARED_LIBS:  ON 
> #CMAKE_INSTALL_PREFIX:   
> /Applications/deal.II-9.0-spack.app/Contents/Resources 
> #CMAKE_SOURCE_DIR:   /Users/heltai/dealii/dealii 
> #(version 9.0.0-pre, shortrev 88babf1a4d) 
> #CMAKE_BINARY_DIR:   
> /Users/heltai/dealii/dealii/build-9.0-spack 
> #CMAKE_CXX_COMPILER: AppleClang 9.0.0.938 on platform 
> Darwin x86_64 
> #   
>  /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/bin/mpic++ 
>
> # 
> #  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, 
> DEAL_II_ALLOW_AUTODETECTION = ON): 
> #  ( DEAL_II_WITH_64BIT_INDICES = OFF ) 
> #DEAL_II_WITH_ADOLC set up with external dependencies 
> #DEAL_II_WITH_ARPACK set up with external dependencies 
> #DEAL_II_WITH_ASSIMP set up with external dependencies 
> #DEAL_II_WITH_BOOST set up with external dependencies 
> #  ( DEAL_II_WITH_CUDA = OFF ) 
> #DEAL_II_WITH_CXX14 = ON 
> #DEAL_II_WITH_CXX17 = ON 
> #DEAL_II_WITH_GSL set up with external dependencies 
> #DEAL_II_WITH_HDF5 set up with external dependencies 
> #DEAL_II_WITH_LAPACK set up with external dependencies 
> #DEAL_II_WITH_METIS set up with external dependencies 
> #DEAL_II_WITH_MPI set up with external dependencies 
> #DEAL_II_WITH_MUPARSER set up with external dependencies 
> #DEAL_II_WITH_NANOFLANN set up with external dependencies 
> #DEAL_II_WITH_NETCDF set up with external dependencies 
> #DEAL_II_WITH_OPENCASCADE set up with external dependencies 
> #DEAL_II_WITH_P4EST set up with external dependencies 
> #DEAL_II_WITH_PETSC set up with external dependencies 
> #DEAL_II_WITH_SLEPC set up with external dependencies 
> #DEAL_II_WITH_SUNDIALS set up with external dependencies 
> #DEAL_II_WITH_THREADS set up with external dependencies 
> #DEAL_II_WITH_TRILINOS set up with external dependencies 
> #DEAL_II_WITH_UMFPACK set up with external dependencies 
> #DEAL_II_WITH_ZLIB set up with external dependencies 
> # 
> #  Component configuration: 
> #  ( DEAL_II_COMPONENT_DOCUMENTATION = OFF ) 
> #  ( DEAL_II_COMPONENT_EXAMPLES = OFF ) 
> #DEAL_II_COMPONENT_PACKAGE 
> #  ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF ) 
> # 
> #  Detailed information (compiler flags, feature configuration) can be 
> found in detailed.log 
> # 
> #  Run  $ ninja info  to print a help message with a list of top level 
> targets 
> # 
> ### 
>
> And this is the output of spack find: 
>
> ==> 74 installed packages. 
> -- darwin-highsierra-x86_64 / clang@9.0.0-apple - 
> adol-c@develop  freetype@2.7.1lcms@2.8 
> nasm@2.11.06pkg-config@0.29.2 
> arpack-ng@3.5.0 gcc@7.2.0 libjpeg-turbo@1.5.0 
>  ncurses@6.0 python@2.7.14 
> assimp@4.0.1gdbm@1.13 libpng@1.6.29
> net...@4.4.1.1   readline@7.0 
> astyle@2.04 get...@0.19.8.1  
>  libsigsegv@2.11  netcdf-cxx@4.2  slepc@3.8.0 
> autoconf@2.69   ghostscript@9.21  libtiff@4.0.8   
>  netlib-scalapack@2.0.2  sqlite@3.20.0 
> automake@1.15.1 g...@0.9.7.1
> libtool@2.4.6ninja@1.8.2 suite-sparse@4.5.5 
> bison@3.0.4 gmp@6.1.2 libxml2@2.9.4   
>  numdiff@5.9.0   sundials@3.0.0 
> boost@1.63.0graphviz@2.38.0   m4@1.4.18   
>  oce@0.18.2  superlu-dist@5.2.2 
> bzip2@1.0.6 gsl@2.4   matio@1.5.9 
>  openblas@0.2.20 tar@1.29 
> cmake@3.9.4 hdf5@1.10.1   metis@5.1.0 
>  openmpi@3.0.0   tcl@8.6.6 
> dealii@develop  help2man@1.47.4   mpc@1.0.3   
>  openssl@1.0.2k  trilinos@12.12.1 
> doxygen@1.8.12  hwloc@1.11.8  mpfr@3.1.5   
> p4est@2.0   xz@5.2.3 
> 

Re: [deal.II] query FE support point type and additional info?

[Wolfgang Bangerth]

You can't. There is no obvious relationship between the two for
*generalized* support points. There may be more, or fewer generalized
support points than DoFs on a cell.


Of course there is no obvious relationship but I would assume that
there is some relationship between them (not necessarily unique in any
direction). I guess you are saying is that we are currently not
exposing any relationship between them.


It's all essentially internal to the FE classes. The FE class exports 
where it likes stuff to be evaluated (these are the generalized support 
points) but how it uses the resulting vector of values to obtain DoF 
values is up to the internals of the FE class again. The two places (the 
description of where the generalized support points are, and the place 
that converts function values at generalized support points to DoF 
values) just need to agree on the order of points. But because both of 
these are in the same class, they may choose any perturbation of points. 
A FE may also describe more support point that it then decides to not 
use. There really is not required relationship between the two.


In other words, it's up to every FE to decide what it wants things to 
be. Some FEs may have more generalized support points than DoFs, others 
less.




The reason I am asking is that I would like to differentiate between a
generalized support point in the interior of the cell that just
happens to be on a face and a face dof (for example FE_DGQ vs FE_Q).


This question does not make sense. If you have a modal (as opposed to 
nodal) element, then *all* generalized support points will be used in 
determining *each* modal DoF value. You cannot say that some generalized 
support points are associated with specific DoFs.




get_associated_geometry_primitive answers this for DoFs, but it looks
like I am out of luck tying this back to support point locations
unless I have n_dofs_per_cell unit_support_points and no
generalized_support_points. So I can do this for FE_DGQ but not for
Nedelec or other elements. Does that sound about right? I was hoping
there is an easy way to query this information.


Yes, this is correct. No easy way -- in fact: no way, period -- because 
there is no relationship.




3. Elements like FE_QLegendre return 0 generalized support points. Is
there any information I can extract from the FE about the degrees of
freedom or support points in this case?


I should say that the fact that FE_QLegendre doesn't publish GSPs is 
functionality that is missing, not because it can't define them. It's 
just that nobody has implemented this so far.


Best
 W>

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

--
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Re: [deal.II] New Mac OSX brew package

[Timo Heister]

thanks, Luca!

Are you using the system clang with the fortran compiler from gcc? Are
the spack packages compiled with gcc or with clang?

On Thu, Nov 9, 2017 at 3:40 AM, luca.heltai  wrote:
> Dear All,
>
> I just finished uploading a new brew based package for deal.II with a 
> 9.0pre.1 version:
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_luca-2Dheltai_dealii_releases_tag_v9.0.pre.1=DwIFaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=B4_I7m9Fb7UJr3fQ0YmopMCt2BsnKOY2uoFIQ28VKXs=UQTroVQ4XmKFbV4qTi4pGa6KPdjCdxglDVCGB7IPIo4=
>  
>
> It was compiled on a Mac OS X High Sierra: 10.13 (17A405), with Xcode 9.0.1 
> (9A1004).
>
> The application contains a full `spack` installation at
>
> `/Applications/deal.II-9.0-spack/Contents/Resources/spack`
>
> You’ll have access to all spack facilities (including modules) by adding
>
> . 
> /Applications/deal.II-9.0-spack.app/Contents/Resources/share/deal.II/dealii.conf
>
> to your ~/.profile file.
>
> Summary.log:
>
> ###
> #
> #  deal.II configuration:
> #CMAKE_BUILD_TYPE:   DebugRelease
> #BUILD_SHARED_LIBS:  ON
> #CMAKE_INSTALL_PREFIX:   
> /Applications/deal.II-9.0-spack.app/Contents/Resources
> #CMAKE_SOURCE_DIR:   /Users/heltai/dealii/dealii
> #(version 9.0.0-pre, shortrev 88babf1a4d)
> #CMAKE_BINARY_DIR:   /Users/heltai/dealii/dealii/build-9.0-spack
> #CMAKE_CXX_COMPILER: AppleClang 9.0.0.938 on platform Darwin 
> x86_64
> #
> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/bin/mpic++
> #
> #  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, 
> DEAL_II_ALLOW_AUTODETECTION = ON):
> #  ( DEAL_II_WITH_64BIT_INDICES = OFF )
> #DEAL_II_WITH_ADOLC set up with external dependencies
> #DEAL_II_WITH_ARPACK set up with external dependencies
> #DEAL_II_WITH_ASSIMP set up with external dependencies
> #DEAL_II_WITH_BOOST set up with external dependencies
> #  ( DEAL_II_WITH_CUDA = OFF )
> #DEAL_II_WITH_CXX14 = ON
> #DEAL_II_WITH_CXX17 = ON
> #DEAL_II_WITH_GSL set up with external dependencies
> #DEAL_II_WITH_HDF5 set up with external dependencies
> #DEAL_II_WITH_LAPACK set up with external dependencies
> #DEAL_II_WITH_METIS set up with external dependencies
> #DEAL_II_WITH_MPI set up with external dependencies
> #DEAL_II_WITH_MUPARSER set up with external dependencies
> #DEAL_II_WITH_NANOFLANN set up with external dependencies
> #DEAL_II_WITH_NETCDF set up with external dependencies
> #DEAL_II_WITH_OPENCASCADE set up with external dependencies
> #DEAL_II_WITH_P4EST set up with external dependencies
> #DEAL_II_WITH_PETSC set up with external dependencies
> #DEAL_II_WITH_SLEPC set up with external dependencies
> #DEAL_II_WITH_SUNDIALS set up with external dependencies
> #DEAL_II_WITH_THREADS set up with external dependencies
> #DEAL_II_WITH_TRILINOS set up with external dependencies
> #DEAL_II_WITH_UMFPACK set up with external dependencies
> #DEAL_II_WITH_ZLIB set up with external dependencies
> #
> #  Component configuration:
> #  ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
> #  ( DEAL_II_COMPONENT_EXAMPLES = OFF )
> #DEAL_II_COMPONENT_PACKAGE
> #  ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
> #
> #  Detailed information (compiler flags, feature configuration) can be found 
> in detailed.log
> #
> #  Run  $ ninja info  to print a help message with a list of top level targets
> #
> ###
>
> And this is the output of spack find:
>
> ==> 74 installed packages.
> -- darwin-highsierra-x86_64 / clang@9.0.0-apple -
> adol-c@develop  freetype@2.7.1lcms@2.8 
> nasm@2.11.06pkg-config@0.29.2
> arpack-ng@3.5.0 gcc@7.2.0 libjpeg-turbo@1.5.0  
> ncurses@6.0 python@2.7.14
> assimp@4.0.1gdbm@1.13 libpng@1.6.29
> netcdf@4.4.1.1  readline@7.0
> astyle@2.04 gettext@0.19.8.1  libsigsegv@2.11  
> netcdf-cxx@4.2  slepc@3.8.0
> autoconf@2.69   ghostscript@9.21  libtiff@4.0.8
> netlib-scalapack@2.0.2  sqlite@3.20.0
> automake@1.15.1 glm@0.9.7.1   libtool@2.4.6
> ninja@1.8.2 suite-sparse@4.5.5
> bison@3.0.4 gmp@6.1.2 libxml2@2.9.4
> numdiff@5.9.0   sundials@3.0.0
> boost@1.63.0graphviz@2.38.0   m4@1.4.18oce@0.18.2 
>  superlu-dist@5.2.2
> bzip2@1.0.6 gsl@2.4   matio@1.5.9  
> openblas@0.2.20 tar@1.29
> cmake@3.9.4 hdf5@1.10.1   metis@5.1.0  
> openmpi@3.0.0   tcl@8.6.6
> dealii@develop  

Re: [deal.II] query FE support point type and additional info?

[Timo Heister]

thanks, Wolfgang.

>> 1. How can I translate between generalized_support_point j and
>> dof_per_cell index k? For example FE_DGRaviartThomas<2>(1) has 9
>> generalized_support_points but 12 dofs_per_cell.
>
> You can't. There is no obvious relationship between the two for
> *generalized* support points. There may be more, or fewer generalized
> support points than DoFs on a cell.

Of course there is no obvious relationship but I would assume that
there is some relationship between them (not necessarily unique in any
direction). I guess you are saying is that we are currently not
exposing any relationship between them.

The reason I am asking is that I would like to differentiate between a
generalized support point in the interior of the cell that just
happens to be on a face and a face dof (for example FE_DGQ vs FE_Q).
get_associated_geometry_primitive answers this for DoFs, but it looks
like I am out of luck tying this back to support point locations
unless I have n_dofs_per_cell unit_support_points and no
generalized_support_points. So I can do this for FE_DGQ but not for
Nedelec or other elements. Does that sound about right? I was hoping
there is an easy way to query this information.

>> 3. Elements like FE_QLegendre return 0 generalized support points. Is
>> there any information I can extract from the FE about the degrees of
>> freedom or support points in this case?
>
> Nope :-) That's generally true for all elements that don't have (regular)
> support points: they're not interpolatory, and so may define their shape
> functions in whatever way they choose.

I found get_associated_geometry_primitive(dof_idx), which tells us at
least something about the shape functions. I can also check if the
functions are primitive or not, but that seems to be it.

-- 
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Re: [deal.II] Interpolation from one grid to another external grid from LinearAlgebraTrilinos::MPI::Vector

[Wolfgang Bangerth]

On 11/09/2017 09:14 AM, 'Maxi Miller' via deal.II User Group wrote:
I am calculating a wave propagation over my grid, using a DHT (discrete hankel 
transformation) for the propagation. Can this method be included in an 
existing project? It would need a special grid spacing defined by the roots of 
the bessel function in one direction, and a regular spacing in the second (cf 
Kai-Ming, Y., Shuang-Chun, W., Lie-Zun, C., You-Wen, W., & Yong-Hua, H. 
(2009). A quasi-discrete Hankel transform for nonlinear beam propagation. 
/Chinese Physics B/, /18/(9), 3893–3899. 
https://doi.org/10.1088/1674-1056/18/9/046). Else it results in 
vector-vector-multiplications and matrix-vector-multiplications, which can be 
done in deal.II. Do you have something which can keep the grids within 
deal.II, even though I have to use two different grids now (one for a full 
matrix for the propagation, one from the original program in deal.II)?


*Any* interpolation between grids is expensive. It doesn't matter whether they 
are both managed by deal.II.


But if they both happen to be managed by deal.II, then a combination of
  FEFieldFunction
  VectorTools::interpolate
will make the process simple (though not efficient).

Best
 W.


--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

--
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Re: [deal.II] Interpolation from one grid to another external grid from LinearAlgebraTrilinos::MPI::Vector

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

I am calculating a wave propagation over my grid, using a DHT (discrete 
hankel transformation) for the propagation. Can this method be included in 
an existing project? It would need a special grid spacing defined by the 
roots of the bessel function in one direction, and a regular spacing in the 
second (cf Kai-Ming, Y., Shuang-Chun, W., Lie-Zun, C., You-Wen, W., & 
Yong-Hua, H. (2009). A quasi-discrete Hankel transform for nonlinear beam 
propagation. *Chinese Physics B*, *18*(9), 3893–3899. 
https://doi.org/10.1088/1674-1056/18/9/046). Else it results in 
vector-vector-multiplications and matrix-vector-multiplications, which can 
be done in deal.II. Do you have something which can keep the grids within 
deal.II, even though I have to use two different grids now (one for a full 
matrix for the propagation, one from the original program in deal.II)?

 D

Am Donnerstag, 9. November 2017 16:20:34 UTC+1 schrieb Wolfgang Bangerth:
>
> On 11/09/2017 01:46 AM, 'Maxi Miller' via deal.II User Group wrote: 
> > In a current project I am coupling an external calculation (consisting 
> out of 
> > several matrix- and vector multiplications) to my deal.II-calculations. 
> For 
> > that I have to transfer the solution from deal.II to my other 
> calculations, 
> > process it there, and transfer the result back. Thus I am now looking 
> for a 
> > way to transfer the solution from deal.II (from a MPI::Vector) onto a 
> matrix 
> > using a different coordinate system (currently written in Armadillo, but 
> can 
> > be changed if necessary). One approach I would have thought of is to 
> loop over 
> > all the q-points in the solution, write them into a matrix, and then use 
> a 
> > spline interpolation to fill the matrix used for calculations. But is 
> there a 
> > better way to do that? 
> > I can also try to also write the calculations directly in deal.II, but 
> then I 
> > still have the problem of interpolating from one coordinate system to 
> another. 
> > Or is there a function in deal.II to interpolate from one grid (which is 
> > created within deal.II) to another (which is created using external 
> methods)? 
> > The interpolation-methods I found until now all require a second 
> dof-handler, 
> > which I do not have. 
>
> Interpolating from one mesh to an unrelated, separate one is a really 
> expensive operation. If you can at all avoid this, then you should. 
>
> If you must do it, then take a look at the FEFieldFunction class. It makes 
> your finite element solution look like a regular function that you can 
> evaluate in your interpolation operation. But because it's expensive to 
> evaluate at arbitrary points, be prepared for this to be a slow process if 
> you 
> have many cells on both meshes. 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

-- 
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Re: [deal.II] query FE support point type and additional info?

[Wolfgang Bangerth]

I am looking for ways to get more information about (generalized)
support points for a particular FE:
1. How can I translate between generalized_support_point j and
dof_per_cell index k? For example FE_DGRaviartThomas<2>(1) has 9
generalized_support_points but 12 dofs_per_cell.


You can't. There is no obvious relationship between the two for *generalized* 
support points. There may be more, or fewer generalized support points than 
DoFs on a cell.




2. 
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_developer_doxygen_deal.II_DEALGlossary.html-23GlossGeneralizedSupport=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=noUPzp6HQo5Ab1sMhXHEPDtKWiunYMqmACzbvcvljEk=xGxO7IMz8sGBENTwwyRKlCiJ7WNuI0hby0Co0ZQhaks=
says FE_Q_Hierarchical has no generalized support points but the
element actually returns 4 generalized support points in 2d with
degree 1. Who is right?


The code. We further generalized generalized support points a while back, see
  https://github.com/dealii/dealii/issues/4992
The glossary entry needs to be updated.



3. Elements like FE_QLegendre return 0 generalized support points. Is
there any information I can extract from the FE about the degrees of
freedom or support points in this case?


Nope :-) That's generally true for all elements that don't have (regular) 
support points: they're not interpolatory, and so may define their shape 
functions in whatever way they choose.


Best
 W.


--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

--
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Re: [deal.II] Interpolation from one grid to another external grid from LinearAlgebraTrilinos::MPI::Vector

[Wolfgang Bangerth]

On 11/09/2017 01:46 AM, 'Maxi Miller' via deal.II User Group wrote:
In a current project I am coupling an external calculation (consisting out of 
several matrix- and vector multiplications) to my deal.II-calculations. For 
that I have to transfer the solution from deal.II to my other calculations, 
process it there, and transfer the result back. Thus I am now looking for a 
way to transfer the solution from deal.II (from a MPI::Vector) onto a matrix 
using a different coordinate system (currently written in Armadillo, but can 
be changed if necessary). One approach I would have thought of is to loop over 
all the q-points in the solution, write them into a matrix, and then use a 
spline interpolation to fill the matrix used for calculations. But is there a 
better way to do that?
I can also try to also write the calculations directly in deal.II, but then I 
still have the problem of interpolating from one coordinate system to another. 
Or is there a function in deal.II to interpolate from one grid (which is 
created within deal.II) to another (which is created using external methods)? 
The interpolation-methods I found until now all require a second dof-handler, 
which I do not have.


Interpolating from one mesh to an unrelated, separate one is a really 
expensive operation. If you can at all avoid this, then you should.


If you must do it, then take a look at the FEFieldFunction class. It makes 
your finite element solution look like a regular function that you can 
evaluate in your interpolation operation. But because it's expensive to 
evaluate at arbitrary points, be prepared for this to be a slow process if you 
have many cells on both meshes.


Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] A_inverse in step-57

[Wolfgang Bangerth]

Jie,

It turns out the SparseILU needs to be tuned very carefully. I set the 
AdditioalData to (0.03, 0) the solver now works fine. Although it is still 
slower than UMFPACK. Maybe using just the right parameters in AdditionalData 
can further improve it. I observed similar thing in step-57 too. Using ILU + 
GMRES for A inverse won't even converge in reasonable time with default 
AdditionalData. Playing with the AdditionalData helps... In a word, SparseILU 
seems to be sensitive to the AdditionalData and how to choose the right 
parameter is unclear.


Yes, that's what I meant to say in my last email: the ILU is quite sensitive 
to choosing parameters.


Do you have a set of parameters that works significantly better than what we 
currently use in step-57? Would you like to propose we make changes to step-57 
in this direction?



Wolfgang, would you like me to contribute this code to the code gallery? Is 
there anything in this code that I should polish?


You mean your time-dependent N-S solver? Yes, we would absolutely love to have 
it as part of the code gallery! If you contribute it as a pull request as 
explained on the website, we can take a look and see what should/needs to be 
polished, though we're typically quite relaxed about code gallery programs!


Best
 Wolfgang

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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[deal.II] New Mac OSX brew package

[luca . heltai]

Dear All, 

I just finished uploading a new brew based package for deal.II with a 9.0pre.1 
version:

https://github.com/luca-heltai/dealii/releases/tag/v9.0.pre.1

It was compiled on a Mac OS X High Sierra: 10.13 (17A405), with Xcode 9.0.1 
(9A1004).

The application contains a full `spack` installation at 

`/Applications/deal.II-9.0-spack/Contents/Resources/spack`

You’ll have access to all spack facilities (including modules) by adding

. 
/Applications/deal.II-9.0-spack.app/Contents/Resources/share/deal.II/dealii.conf
 

to your ~/.profile file.

Summary.log:

###
#
#  deal.II configuration:
#CMAKE_BUILD_TYPE:   DebugRelease
#BUILD_SHARED_LIBS:  ON
#CMAKE_INSTALL_PREFIX:   
/Applications/deal.II-9.0-spack.app/Contents/Resources
#CMAKE_SOURCE_DIR:   /Users/heltai/dealii/dealii
#(version 9.0.0-pre, shortrev 88babf1a4d)
#CMAKE_BINARY_DIR:   /Users/heltai/dealii/dealii/build-9.0-spack
#CMAKE_CXX_COMPILER: AppleClang 9.0.0.938 on platform Darwin 
x86_64
#
/Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/bin/mpic++
#
#  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION 
= ON):
#  ( DEAL_II_WITH_64BIT_INDICES = OFF )
#DEAL_II_WITH_ADOLC set up with external dependencies
#DEAL_II_WITH_ARPACK set up with external dependencies
#DEAL_II_WITH_ASSIMP set up with external dependencies
#DEAL_II_WITH_BOOST set up with external dependencies
#  ( DEAL_II_WITH_CUDA = OFF )
#DEAL_II_WITH_CXX14 = ON
#DEAL_II_WITH_CXX17 = ON
#DEAL_II_WITH_GSL set up with external dependencies
#DEAL_II_WITH_HDF5 set up with external dependencies
#DEAL_II_WITH_LAPACK set up with external dependencies
#DEAL_II_WITH_METIS set up with external dependencies
#DEAL_II_WITH_MPI set up with external dependencies
#DEAL_II_WITH_MUPARSER set up with external dependencies
#DEAL_II_WITH_NANOFLANN set up with external dependencies
#DEAL_II_WITH_NETCDF set up with external dependencies
#DEAL_II_WITH_OPENCASCADE set up with external dependencies
#DEAL_II_WITH_P4EST set up with external dependencies
#DEAL_II_WITH_PETSC set up with external dependencies
#DEAL_II_WITH_SLEPC set up with external dependencies
#DEAL_II_WITH_SUNDIALS set up with external dependencies
#DEAL_II_WITH_THREADS set up with external dependencies
#DEAL_II_WITH_TRILINOS set up with external dependencies
#DEAL_II_WITH_UMFPACK set up with external dependencies
#DEAL_II_WITH_ZLIB set up with external dependencies
#
#  Component configuration:
#  ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
#  ( DEAL_II_COMPONENT_EXAMPLES = OFF )
#DEAL_II_COMPONENT_PACKAGE
#  ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
#
#  Detailed information (compiler flags, feature configuration) can be found in 
detailed.log
#
#  Run  $ ninja info  to print a help message with a list of top level targets
#
###

And this is the output of spack find:

==> 74 installed packages.
-- darwin-highsierra-x86_64 / clang@9.0.0-apple -
adol-c@develop  freetype@2.7.1lcms@2.8 nasm@2.11.06 
   pkg-config@0.29.2
arpack-ng@3.5.0 gcc@7.2.0 libjpeg-turbo@1.5.0  ncurses@6.0  
   python@2.7.14
assimp@4.0.1gdbm@1.13 libpng@1.6.29
netcdf@4.4.1.1  readline@7.0
astyle@2.04 gettext@0.19.8.1  libsigsegv@2.11  
netcdf-cxx@4.2  slepc@3.8.0
autoconf@2.69   ghostscript@9.21  libtiff@4.0.8
netlib-scalapack@2.0.2  sqlite@3.20.0
automake@1.15.1 glm@0.9.7.1   libtool@2.4.6ninja@1.8.2  
   suite-sparse@4.5.5
bison@3.0.4 gmp@6.1.2 libxml2@2.9.4
numdiff@5.9.0   sundials@3.0.0
boost@1.63.0graphviz@2.38.0   m4@1.4.18oce@0.18.2   
   superlu-dist@5.2.2
bzip2@1.0.6 gsl@2.4   matio@1.5.9  
openblas@0.2.20 tar@1.29
cmake@3.9.4 hdf5@1.10.1   metis@5.1.0  
openmpi@3.0.0   tcl@8.6.6
dealii@develop  help2man@1.47.4   mpc@1.0.3
openssl@1.0.2k  trilinos@12.12.1
doxygen@1.8.12  hwloc@1.11.8  mpfr@3.1.5   p4est@2.0
   xz@5.2.3
environment-modules@3.2.10  hypre@2.12.1  mumps@5.1.1  
parmetis@4.0.3  zip@3.0
expat@2.2.2 intel-tbb@2018.1  muparser@2.2.5   perl@5.24.1  
   zlib@1.2.11
flex@2.6.4  isl@0.18  nanoflann@1.2.3  petsc@3.8.1

You can also load individual module files.

module avail:
bash-3.2$ module avail

-