deal.II on Mac OS Sierra

Pawan Takhar

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Oct 24, 2017, 9:22:46 PM10/24/17

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I am a new user of deal.II. I installed 8.5.0 on Mac OS Sierra a few months ago. I used .dmg and cmake .dmg files and set the environment variables as suggested on website. The program was running fine but at some time, maybe after update of Xcode, I have started getting the following error. I have performed a fresh installation on a different computer, but still this error does not go away. The error originates when I run the make in command window.

cmake . runs without any problem. When I run make I get the following warnings and errors. Please help.

Thanks,

Pawan

In file included from /Applications/deal.II-8.5-brew.app/Contents/Resources/examples/step-1/step-1.cc:22:

/Applications/deal.II-8.5-brew.app/Contents/Resources/include/deal.II/grid/tria.h:31:1: warning:

unknown warning group '-Wunused-but-set-parameter', ignored

[-Wunknown-warning-option]

DEAL_II_DISABLE_EXTRA_DIAGNOSTICS

^

/Applications/deal.II-8.5-brew.app/Contents/Resources/include/deal.II/base/config.h:307:66: note:

expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'

_Pragma("GCC diagnostic ignored \"-Winfinite-recursion\"") \

^

<scratch space>:60:25: note: expanded from here

GCC diagnostic ignored "-Wunused-but-set-parameter"

^

In file included from /Applications/deal.II-8.5-brew.app/Contents/Resources/examples/step-1/step-1.cc:22:

/Applications/deal.II-8.5-brew.app/Contents/Resources/include/deal.II/grid/tria.h:31:1: warning:

unknown warning group '-Wunused-but-set-variable', ignored

[-Wunknown-warning-option]

/Applications/deal.II-8.5-brew.app/Contents/Resources/include/deal.II/base/config.h:311:66: note:

expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'

_Pragma("GCC diagnostic ignored \"-Wdeprecated-declarations\"") \

^

<scratch space>:61:25: note: expanded from here

GCC diagnostic ignored "-Wunused-but-set-variable"

^

In file included from /Applications/deal.II-8.5-brew.app/Contents/Resources/examples/step-1/step-1.cc:22:

/Applications/deal.II-8.5-brew.app/Contents/Resources/include/deal.II/grid/tria.h:31:1: warning:

unknown warning group '-Wexpansion-to-defined', ignored

[-Wunknown-warning-option]

/Applications/deal.II-8.5-brew.app/Contents/Resources/include/deal.II/base/config.h:312:66: note:

expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'

_Pragma("GCC diagnostic ignored \"-Wunused-but-set-variable\"") \

^

<scratch space>:61:25: note: expanded from here

GCC diagnostic ignored "-Wexpansion-to-defined"

^

In file included from /Applications/deal.II-8.5-brew.app/Contents/Resources/examples/step-1/step-1.cc:22:

/Applications/deal.II-8.5-brew.app/Contents/Resources/include/deal.II/grid/tria.h:31:1: warning:

unknown warning group '-Wmisleading-indentation', ignored

[-Wunknown-warning-option]

/Applications/deal.II-8.5-brew.app/Contents/Resources/include/deal.II/base/config.h:314:66: note:

expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'

_Pragma("GCC diagnostic ignored \"-Wignored-attributes\"") \

^

<scratch space>:61:25: note: expanded from here

GCC diagnostic ignored "-Wmisleading-indentation"

^

4 warnings generated.

make[2]: *** No rule to make target `/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/System/Library/Frameworks/Accelerate.framework', needed by `step-1'. Stop.

make[1]: *** [CMakeFiles/step-1.dir/all] Error 2

make: *** [all] Error 2

Alberto Salvadori

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Oct 24, 2017, 10:09:32 PM10/24/17

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Hi Pawan,

This issue has been dealt with in

https://groups.google.com/forum/m/#!topic/dealii/KypFL9X0bVo

Best,

Alberto

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Pawan Takhar

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Oct 27, 2017, 9:37:20 AM10/27/17

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Alberto,

Thanks for your reply. I installed 10.12 SDK as suggested in previous discussion. I also set the project to use 10.12. Now when I build from within Xcode, the project is compiling fine, but I get the following warning

DEAL_II_DISABLE_EXTRA_DIAGNOSTICS "Unknown warning group '-Wunused-but-set-variable', ignored".

The steps I am using are:

1) cmake . -G "Xcode"

2) open the project in Xcode

3) Change Base SDK to macOS 10.12

4) Build the project.

Thanks,

Pawan

Timo Heister

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Oct 27, 2017, 12:45:35 PM10/27/17

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great to hear that this works. I am in the process to create a second
installer for the newer xcode+sdk.

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Pawan Takhar

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Oct 31, 2017, 12:46:38 PM10/31/17

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Thanks for compiling the newer version of .dmg file, Timo. I tried compiling 8.5.1 .tar.gz file, but make failed on that as well with newer versions of MacOS. I look forward to your .dmg file.

Regards,

Pawan

Uwe Köcher

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Nov 1, 2017, 5:00:07 AM11/1/17

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Hej Pawan,

I tried compiling 8.5.1 .tar.gz file, but make failed on that as well with newer versions of MacOS. I look forward to your .dmg file.

you can try to use the candi installer for deal.II

https://github.com/dealii/candi

With that, it was possible to compile deal.II with dependencies on a Mac. The installation even worked after the latest Xcode upgrade and the upgrade to HighSierra.

Kind regards

Uwe

Message has been deleted

Pawan Takhar

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Nov 7, 2017, 11:32:43 PM11/7/17

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Hi Uwe,

I tried installing using Candi installer, but unfortunately it did not work for me. The application installed without any errors. However when I use the following commands I get error in the second and third steps:

1) cmake . (It is able to find the dealII-candi as I have included it in the path)

2) make (numerous errors/warning message on this step. I am pasting those below.

.3) /step-1 (does not run).

I hope someone would compile .dmg file for the macOS High Sierra.

Thanks,

Pawan

Warning/error messages:

Scanning dependencies of target step-1

[ 50%] Building CXX object CMakeFiles/step-1.dir/step-1.cc.o

In file included from /Users/username/Documents/deal2/examples/step1/step-1.cc:22:

/Users/user/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: warning:

unknown warning group '-Wunused-but-set-parameter', ignored

[-Wunknown-warning-option]

DEAL_II_DISABLE_EXTRA_DIAGNOSTICS

^

/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:307:66: note:

expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'

_Pragma("GCC diagnostic ignored \"-Winfinite-recursion\"") \

^

<scratch space>:44:25: note: expanded from here

GCC diagnostic ignored "-Wunused-but-set-parameter"

^

In file included from /Users/username/Documents/deal2/examples/step1/step-1.cc:22:

/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: warning:

unknown warning group '-Wunused-but-set-variable', ignored

[-Wunknown-warning-option]

/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:311:66: note:

expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'

_Pragma("GCC diagnostic ignored \"-Wdeprecated-declarations\"") \

^

<scratch space>:45:25: note: expanded from here

GCC diagnostic ignored "-Wunused-but-set-variable"

^

In file included from /Users/username/Documents/deal2/examples/step1/step-1.cc:22:

/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: warning:

unknown warning group '-Wexpansion-to-defined', ignored

[-Wunknown-warning-option]

/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:312:66: note:

expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'

_Pragma("GCC diagnostic ignored \"-Wunused-but-set-variable\"") \

^

<scratch space>:45:25: note: expanded from here

GCC diagnostic ignored "-Wexpansion-to-defined"

^

In file included from /Users/username/Documents/deal2/examples/step1/step-1.cc:22:

/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: warning:

unknown warning group '-Wmisleading-indentation', ignored

[-Wunknown-warning-option]

/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:314:66: note:

expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'

_Pragma("GCC diagnostic ignored \"-Wignored-attributes\"") \

^

<scratch space>:45:25: note: expanded from here

GCC diagnostic ignored "-Wmisleading-indentation"

^

In file included from /Users/username/Documents/deal2/examples/step1/step-1.cc:22:

/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: warning:

unknown warning group '-Wint-in-bool-context', ignored

[-Wunknown-warning-option]

/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:318:66: note:

expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'

_Pragma("GCC diagnostic ignored \"-Wimplicit-fallthrough\"") \

^

<scratch space>:45:25: note: expanded from here

GCC diagnostic ignored "-Wint-in-bool-context"

^

5 warnings generated.

[100%] Linking CXX executable step-1

[100%] Built target step-1

Uwe Köcher

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Nov 8, 2017, 4:42:36 AM11/8/17

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Hi Pawan,

what do you mean by

.3) /step-1 (does not run).

?

I only can see warnings and 100% Built & Linking, no errors.

Those warnings relates to the apple-clang compiler.

Pawan Takhar

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Nov 8, 2017, 10:52:48 AM11/8/17

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Hi Uwe,

When I type ./step-1 in the folder where step-1 was compiled, I get the following error:

dyld: Library not loaded: libTKBO.11.dylib

Referenced from: /Users/username/Documents/deal2/examples/step1/./step-1

Reason: image not found

Abort trap: 6

I tried searching for libTKBO.11.dylib, but could not find the package that would contain this.

Regards,

Pawan

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Uwe Köcher

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Nov 8, 2017, 11:20:42 AM11/8/17

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ah, it seems that you have installed oce as well... I've checked my modulefile for macOS, an I set

all the lib-pathes...

depending on the packages you have installed, it should be

export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/OCE-0.18/lib:/apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/parmetis-4.0.3/lib

and so on... each lib path is divided by a colon (:).

Check for your lib-pathes in your installation destination.

You can include that in the "enable.sh" script.

For me, the current complete list (set in a modulefile) is:

prepend-path            DYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/parmetis-4.0.3/lib
prepend-path            DYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/superlu_dist_5.1.2/lib


#prepend-path            DYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/OCE-0.18/lib
prepend-path            DYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/deal.II-v8.5.1/lib
prepend-path            DYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/hdf5-1.10.1/lib
#prepend-path            DYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/p4est-2.0/FAST/lib
#prepend-path            DYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/p4est-2.0/DEBUG/lib
prepend-path            DYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/petsc-3.7.6/lib
prepend-path            DYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/slepc-3.7.3/lib
prepend-path            DYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/trilinos-release-12-10-1/lib

Pawan Takhar

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Nov 9, 2017, 1:23:45 AM11/9/17

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Hi Uwe,

Thanks for providing such a detailed reply. The following suggestion solved my problem.

export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/OCE-0.18/lib:/apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/parmetis-4.0.3/lib

I included this line in my .bash_profile file by using appropriate paths for OCE and parmetis files. Now after compiling the deal-ii programs, when I run them in command line, they run fine. I appreciate your looking into my error messages and troubleshooting.

Regards,

Pawan

From: "'Uwe Köcher' via deal.II User Group" <dea...@googlegroups.com>
Reply-To: <dea...@googlegroups.com>
Date: Wednesday, November 8, 2017 at 10:20 AM
To: "deal.II User Group" <dea...@googlegroups.com>
Subject: Re: [deal.II] deal.II on Mac OS Sierra

export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/OCE-0.18/lib:/apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/parmetis-4.0.3/lib

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