Tutorial fail to run in my enviroment and i need help ....

Hungi

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Jan 5, 2018, 8:03:39 AM1/5/18

to deal.II User Group

Dear Sir

This is the Tutorial step-1 I used and it pass cmake config and build
stage and only it fail on running stage .

I need your help for this failure and your help is appreciated.

regards
hungi

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

hichoudeiMac:examples hichou$ cd step-1

hichoudeiMac:step-1 hichou$ cmake .

-- Autopilot invoked

-- Run $ make info to print a detailed help message

-- Configuring done

-- Generating done

-- Build files have been written to: /Users/hichou/Documents/OpenSourceWare/FEMtool/dealii/examples/step-1

hichoudeiMac:step-1 hichou$ make

Scanning dependencies of target step-1

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

[100%] Linking CXX executable step-1

[100%] Built target step-1

hichoudeiMac:step-1 hichou$ ./step-1

dyld: Symbol not found: _klu_solve

Referenced from: /usr/local/opt/sundials/lib/libsundials_idas.1.dylib

Expected in: flat namespace

in /usr/local/opt/sundials/lib/libsundials_idas.1.dylib

Abort trap: 6

hichoudeiMac:step-1 hichou$

Hungi

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Jan 5, 2018, 9:29:45 AM1/5/18

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after I updateing sundials through Homebrew : failure were changed :

bash-3.2$ ./step-1

dyld: Library not loaded: /usr/local/opt/suite-sparse/lib/libsuitesparseconfig.4.5.5.dylib

Referenced from: /Users/hichou/Documents/OpenSourceWare/FEMTool/dealii/lib/libdeal_II.9.0.0-pre.dylib

Reason: image not found

Abort trap: 6

Hungi於 2018年1月5日星期五 UTC+8下午9時03分39秒寫道：

Bruno Turcksin

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Jan 5, 2018, 9:36:13 AM1/5/18

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Hi,

On Friday, January 5, 2018 at 9:29:45 AM UTC-5, Hungi wrote:

after I updateing sundials through Homebrew : failure were changed :

bash-3.2$ ./step-1

dyld: Library not loaded: /usr/local/opt/suite-sparse/lib/libsuitesparseconfig.4.5.5.dylib

Referenced from: /Users/hichou/Documents/OpenSourceWare/FEMTool/dealii/lib/libdeal_II.9.0.0-pre.dylib

Reason: image not found

Abort trap: 6

This is the same problem that you had with sundials but with UMFPACK. How did you install deal.II?

Best,

Brnuo

Hungi

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Jan 5, 2018, 10:11:25 AM1/5/18

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After I check

/usr/local/opt/suite-sparse/lib/ , I do not have libsuitesparseconfig.4.5.5.dylib but libsuitesparseconfig.5.1.0.dylib and libsuitesparseconfig.5.dylib , libsuitesparseconfig.dylib instead ?

Bruno Turcksin

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Jan 5, 2018, 10:14:51 AM1/5/18

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2018-01-05 10:11 GMT-05:00 Hungi <hungi...@gmail.com>:

/usr/local/opt/suite-sparse/lib/ , I do not have libsuitesparseconfig.4.5.5.dylib but libsuitesparseconfig.5.1.0.dylib and libsuitesparseconfig.5.dylib , libsuitesparseconfig.dylib instead ?

I don't know how you installed deal.II but you did something wrong because deal.II is trying to load libraries that are not your machine.

Best,

Bruno

Jean-Paul Pelteret

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Jan 5, 2018, 10:55:53 AM1/5/18

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To comment further on what Bruno’s said, it looks like you probably need to rebuild and reinstall deal.II again. This will ensure that the latest version of these libraries are detected during the configuration stage.

Best,

Jean-Paul

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Hungi

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Jan 5, 2018, 7:26:38 PM1/5/18

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Hi Bruno

Thanks for your help .

I used to use Dealii-8.5.1 and for some reason it did not work for unknown reason in time , I then rein 8.5.0 install either from dealii git hub repository or from Mac dealii-8.5.0-brew.dmg yet it fail to build.

This morning I try to rein install with Dealii-8.5.1 again , I will notice you with the result.

Bruno Turcksin於 2018年1月5日星期五 UTC+8下午10時36分13秒寫道：

Hungi

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Jan 5, 2018, 7:31:46 PM1/5/18

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Hi Jean_Paul

Thanks for your advice and I am doing rein install process with 8.5.1 now !

will inform you the result.

Jean-Paul Pelteret於 2018年1月5日星期五 UTC+8下午11時55分53秒寫道：

Hungi

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Jan 5, 2018, 11:07:38 PM1/5/18

to deal.II User Group

Hi Bruno

I am kind of mess up !!!

here his the result and it fail even in configuration stage .

result

hichoudeiMac:step-1 hichou$ cmake .

CMake Error at CMakeLists.txt:30 (MESSAGE):

*** Could not locate a (sufficiently recent) version of deal.II. ***

You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to cmake

or set an environment variable "DEAL_II_DIR" that contains this path.

-- Configuring incomplete, errors occurred!

when I try to locate my path to deal.II as requested , I even could not find deal.II in /usr/local directory ( where it is assigned by me to install deal.II).

I list my enviromemnt variable below :

hichoudeiMac:Homebrew hichou$ printenv

DEAL_II_BUNDLE=/Applications/deal.II-8.5-brew.app

TERM_PROGRAM=Apple_Terminal

SHELL=/bin/bash

TERM=xterm-256color

TMPDIR=/var/folders/hf/ylwlk7f94d19njtz1y3jnwdh0000gn/T/

Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.n7KAlzSuIW/Render

TERM_PROGRAM_VERSION=400

OLDPWD=/usr/local

DEAL_II_RESOURCES=/Applications/deal.II-8.5-brew.app/Contents/Resources

TERM_SESSION_ID=1B0D157F-8009-4D86-98FB-6273322E2D2A

USER=hichou

WEB_URL=http://www.coursera.org

SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.9myLObZhUa/Listeners

MACHINE_TYPE=mac-gcc-4.2

GEOS_DIR=/usr/local/geos

PATH=/Users/hichou/Documents/OpenSourceWare/FEMtool/dealii-8.5.1:usr/local/Cellar/gcc/7.2.0/libexec/gcc/x86_64-apple-darwin16.7.0/7.2.0:/Users/hichou/pgmpy:/usr/local/bin:/Users/hichou/Xerces/xerces1.4.3/xerces-1.4.3.jar:/Users/hichou/Documents/Java/XMLJava/samples:/usr/local/Cellar/xerces-c/3.1.4/bin:/usr/local/opt/qt/bin:/Users/hichou/Documents/NWTC/LandBase/FAST_v8.16.00a-bjj/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/X11/bin

PWD=/usr/local/Homebrew

XPC_FLAGS=0x0

XPC_SERVICE_NAME=0

HOME=/Users/hichou

SHLVL=2

LOGNAME=hichou

LC_CTYPE=UTF-8

DISPLAY=/private/tmp/com.apple.launchd.dQ0pZBe2pA/org.macosforge.xquartz:0

_=/usr/bin/printenv

hichoudeiMac:Homebrew hichou$ echo $SHELL

/bin/bash

Just do not know what is possible way to proceed ....

Hungi於 2018年1月6日星期六 UTC+8上午8時26分38秒寫道：

Hungi

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Jan 6, 2018, 12:29:26 AM1/6/18

to deal.II User Group

After running requested make install it showed good sign of progress and

and it pass the make test ( final stage on the installation ) !!!!

So after this , I change to directory of step-1

configure for step-1 program by --> cmake .

hichoudeiMac:step-1 hichou$ cmake .

-- The C compiler identification is AppleClang 9.0.0.9000039

-- The CXX compiler identification is AppleClang 9.0.0.9000039

-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc

-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- 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: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++

-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Autopilot invoked

###

#

# Project step-1 set up with deal.II-8.5.1 found at

# /Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1

#

# 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 sign - to sign the executable with the supplied OSX developer key

#

# $ 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!

#

###

-- Configuring done

-- Generating done

-- Build files have been written to: /Users/hichou/documents/OpenSourceWare/FEMTool/dealii-8.5.1/examples/step-1

Then I use make to build with following warning and progra stop

hichoudeiMac:step-1 hichou$ make

Scanning dependencies of target step-1

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

In file included from /Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/examples/step-1/step-1.cc:22:

/Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/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/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/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>:72:25: note: expanded from here

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

^

In file included from /Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/examples/step-1/step-1.cc:22:

/Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/include/deal.II/grid/tria.h:31:1: warning:

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

[-Wunknown-warning-option]

/Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/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>:73:25: note: expanded from here

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

^

In file included from /Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/examples/step-1/step-1.cc:22:

/Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/include/deal.II/grid/tria.h:31:1: warning:

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

[-Wunknown-warning-option]

/Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/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>:73:25: note: expanded from here

GCC diagnostic ignored "-Wexpansion-to-defined"

^

In file included from /Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/examples/step-1/step-1.cc:22:

/Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/include/deal.II/grid/tria.h:31:1: warning:

unknown warning group '-Wmisleading-indentation', ignored

[-Wunknown-warning-option]

/Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/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>:73:25: note: expanded from here

GCC diagnostic ignored "-Wmisleading-indentation"

^

In file included from /Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/examples/step-1/step-1.cc:22:

/Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/include/deal.II/grid/tria.h:31:1: warning:

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

[-Wunknown-warning-option]

/Users/hichou/documents/OpenSourceWare/FEMtool/dealii-8.5.1/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>:73:25: note: expanded from here

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

^

5 warnings generated.

make[2]: *** No rule to make target `/Users/hichou/Documents/OpenSourceWare/FEMTool/dealii-8.5.1/lib/libdeal_II.g.8.5.1.dylib', needed by `step-1'. Stop.

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

make: *** [all] Error 2

Hungi於 2018年1月6日星期六 UTC+8下午12時07分38秒寫道：

Hungi

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Jan 6, 2018, 5:49:06 AM1/6/18

to deal.II User Group

The issue of -- No rule to make target `/Users/hichou/Documents/OpenSourceWare/FEMTool/dealii-8.5.1/lib/libdeal_II.g.8.5.1.dylib

were resolved by copy libdeal_II.g.8.5.1.dylib /usr/local/lib to /Users/hichou/documents/OpenSourceWare/FEMTool/dealii-8.5.1/lib manually ...

the result were listed below

=================================================================================

hichoudeiMac:step-1 hichou$ make

[ 50%] Linking CXX executable step-1

[100%] Built target step-1

hichoudeiMac:step-1 hichou$ ./step-1

Grid written to grid-1.eps

Grid written to grid-2.eps

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Hungi於 2018年1月6日星期六 UTC+8下午1時29分26秒寫道：

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