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 9.0.0.9000038 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 / cl...@9.0.0-apple -----------------
adol-c@develop free...@2.7.1 lcms@2.8 na...@2.11.06 pkg-c...@0.29.2
arpa...@3.5.0 g...@7.2.0 libjpe...@1.5.0 ncurses@6.0 pyt...@2.7.14
ass...@4.0.1 gd...@1.13 lib...@1.6.29 net...@4.4.1.1 readline@7.0
ast...@2.04 get...@0.19.8.1 libsi...@2.11 netcdf-cxx@4.2 sl...@3.8.0
auto...@2.69 ghost...@9.21 lib...@4.0.8 netlib-s...@2.0.2 sql...@3.20.0
auto...@1.15.1 g...@0.9.7.1 lib...@2.4.6 ni...@1.8.2 suite-...@4.5.5
bi...@3.0.4 g...@6.1.2 lib...@2.9.4 num...@5.9.0 sund...@3.0.0
bo...@1.63.0 grap...@2.38.0 m...@1.4.18 o...@0.18.2 superl...@5.2.2
bz...@1.0.6 gsl@2.4 ma...@1.5.9 open...@0.2.20 t...@1.29
cm...@3.9.4 hd...@1.10.1 me...@5.1.0 ope...@3.0.0 t...@8.6.6
dealii@develop help...@1.47.4 m...@1.0.3 ope...@1.0.2k tril...@12.12.1
dox...@1.8.12 hw...@1.11.8 mp...@3.1.5 p4est@2.0 x...@5.2.3
environme...@3.2.10 hy...@2.12.1 mu...@5.1.1 parm...@4.0.3 zip@3.0
ex...@2.2.2 intel-tbb@2018.1 mupa...@2.2.5 pe...@5.24.1 zl...@1.2.11
fl...@2.6.4 i...@0.18 nano...@1.2.3 pe...@3.8.1

You can also load individual module files.

module avail:
bash-3.2$ module avail

- /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/share/spack/modules/darwin-highsierra-x86_64 --
adol-c/develop ghostscript/9.21 matio/1.5.9 parmetis/4.0.3
arpack-ng/3.5.0 glm/0.9.7.1 metis/5.1.0 perl/5.24.1
assimp/4.0.1 gmp/6.1.2 mpc/1.0.3 petsc/3.8.1
astyle/2.04 graphviz/2.38.0 mpfr/3.1.5 pkg-config/0.29.2
autoconf/2.69 gsl/2.4 mumps/5.1.1 python/2.7.14
automake/1.15.1 hdf5/1.10.1 muparser/2.2.5 readline/7.0
bison/3.0.4 help2man/1.47.4 nanoflann/1.2.3 slepc/3.8.0
boost/1.63.0 hwloc/1.11.8 nasm/2.11.06 sqlite/3.20.0
bzip2/1.0.6 hypre/2.12.1 ncurses/6.0 suite-sparse/4.5.5
cmake/3.9.4 intel-tbb/2018.1 netcdf/4.4.1.1 sundials/3.0.0
dealii/develop isl/0.18 netcdf-cxx/4.2 superlu-dist/5.2.2
doxygen/1.8.12 lcms/2.8 netlib-scalapack/2.0.2 tar/1.29
environment-modules/3.2.10 libjpeg-turbo/1.5.0 ninja/1.8.2 tcl/8.6.6
expat/2.2.2 libpng/1.6.29 numdiff/5.9.0 trilinos/12.12.1
flex/2.6.4 libsigsegv/2.11 oce/0.18.2 xz/5.2.3
freetype/2.7.1 libtiff/4.0.8 openblas/0.2.20 zip/3.0
gcc/7.2.0 libtool/2.4.6 openmpi/3.0.0 zlib/1.2.11
gdbm/1.13 libxml2/2.9.4 openssl/1.0.2k
gettext/0.19.8.1 m4/1.4.18 p4est/2.0

Please, let me know if this works for you.

Best,
Luca.

[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 <luca....@gmail.com> 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&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=B4_I7m9Fb7UJr3fQ0YmopMCt2BsnKOY2uoFIQ28VKXs&s=UQTroVQ4XmKFbV4qTi4pGa6KPdjCdxglDVCGB7IPIo4&e=

> --
> The deal.II project is located at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=B4_I7m9Fb7UJr3fQ0YmopMCt2BsnKOY2uoFIQ28VKXs&s=yUgh1QY1A3RIR9iHpj-Htnn25Zd7WRXfd5Vh8R8-RDg&e=
> For mailing list/forum options, see https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_forum_dealii-3Fhl-3Den&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=B4_I7m9Fb7UJr3fQ0YmopMCt2BsnKOY2uoFIQ28VKXs&s=nWHl0W6CyEu5kJzuxAuCAYqKGT3BLCh8fEk_J0zmuuQ&e=
> ---
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--
Timo Heister
http://www.math.clemson.edu/~heister/

[Denis Davydov]

nice!

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

[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

> 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

> ---
> You received this message because you are subscribed to the Google Groups "deal.II User Group" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to dealii+un...@googlegroups.com.

> For more options, visit https://groups.google.com/d/optout.

[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

[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.

[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 <hei...@clemson.edu> 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.
>

[Denis Davydov]

On 9 Nov 2017, at 23:12, luca.heltai <luca....@gmail.com> 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.

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