Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread yuesu jin 
AH... I understand,* cmake -DCMAKE_INSTALL_PREFIX=[Directory you want to
install] [Directory you build the program]*
I have installed it again in a new folder, the folder now is 3.6GB, which
means something has been installed in that. But the message is still there:
**
[100%] Building CXX object source/CMakeFiles/deal_II.dir/dummy.cc.o
[100%] Linking CXX shared library ../lib/libdeal_II.so
[100%] Built target deal_II
Install the project...
-- Install configuration: "DebugRelease"
CMake Error at cmake/scripts/cmake_install.cmake:36 (file):
  file INSTALL cannot set permissions on
  "/path/to/install/dir/share/deal.II/scripts/normalize.pl"
Call Stack (most recent call first):
  cmake_install.cmake:37 (include)

Makefile:61: recipe for target 'install' failed
make: *** [install] Error 1
**

And when I run make test, all the tests give the same failure message:



/home/yjin6/Deal.II/dealii/tests/quick_tests/gsl.debug: *symbol lookup
error: /home/yjin6/anaconda3/lib/libmkl_intel_lp64.so: undefined symbol:
mkl_blas_dsyrk*
tests/quick_tests/CMakeFiles/gsl.debug.run.dir/build.make:57: recipe for
target 'tests/quick_tests/CMakeFiles/gsl.debug.run' failed
CMakeFiles/Makefile2:7094: recipe for target
'tests/quick_tests/CMakeFiles/gsl.debug.run.dir/all' failed
CMakeFiles/Makefile2:7101: recipe for target
'tests/quick_tests/CMakeFiles/gsl.debug.run.dir/rule' failed
Makefile:2294: recipe for target 'gsl.debug.run' failed
#

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Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread yuesu jin 
Hi Daniel,
  Thank you for your reply. I misunderstood build and install. I thought
after I setup the build folder and make install, the program should be
compiled in that build folder, because I installed the 9.0.1 version just
run the command as those in README file. Now, I first input
*cmake -DCMAKE_INSTALL_PREFIX=/**path/to/install/dir
home/yjin6/Deal.II/dealii-9.0.1  *in
*/home.yjin6/Deal.II/dealii-9.0.1/build, *
then I repeat
*cmake -DCMAKE_INSTALL_PREFIX=${HOME}**/deal.II
/home/yjin6/Deal.II/dealii-9.0.1 *
finally I make install. Is that correct?
Thanks a lot!

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Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread Daniel Arndt 
Yuesu,

Hello Daniel,
>   Thank you very much! I make a new folder to save the compile file for 
> cmake, and I used the command
> *cmake -DCMAKE_INSTALL_PREFIX=${HOME}**/deal.II 
> home/yjin6/Deal.II/dealii-9.0.1* (substituted with my directory),
> but cmake gave error warning. I substitute it with 
> *cmake -DCMAKE_INSTALL_PREFIX=/**path/to/install/dir 
> home/yjin6/Deal.II/dealii-9.0.1*
> Cmake gives the message that:
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/yjin6/Deal.II/dealii
>

This implies that /home/yjin6/Deal.II/dealii is your build directory not 
your installation directory.

cmake -DCMAKE_INSTALL_PREFIX=/home/yjin6/deal.II 
/home/yjin6/Deal.II/dealii-9.0.1

would result in the installation directory to be /home/yjin6/deal.II and 
the build directory to be /home/yjin6/Deal.II/dealii-9.0.1

Best,
Daniel

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Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread yuesu jin 
Hello Daniel,
  Thank you very much! I make a new folder to save the compile file for
cmake, and I used the command
*cmake -DCMAKE_INSTALL_PREFIX=${HOME}**/deal.II
home/yjin6/Deal.II/dealii-9.0.1* (substituted with my directory),
but cmake gave error warning. I substitute it with
*cmake -DCMAKE_INSTALL_PREFIX=/**path/to/install/dir
home/yjin6/Deal.II/dealii-9.0.1*
Cmake gives the message that:
-- Configuring done
-- Generating done
-- Build files have been written to: /home/yjin6/Deal.II/dealii


/home/yjin6/Deal.II/dealii is my current installation directory.
Best regards
Yuesu
On Sun, Aug 11, 2019 at 5:57 PM Daniel Arndt  wrote:

>
> Thank you for your timely reply!
>>  I changed the installation direction according to the README document
>> and redirected it to the deal.ii-9.0.1 source code.
>>
>
> It seems that you still set the installation directory to a non-existent
> path. If you want to install in your home directory calling
>
> cmake -DCMAKE_INSTALL_PREFIX=${HOME}/deal.II DEAL_II_SOURCE_DIR
>
>
> in your build directory should work (you need to replace
> DEAL_II_SOURCE_DIR with the actual path to the deal.II source directory).
>
> Best,
> Daniel
> --
> 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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> 
> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread Daniel Arndt 


> Thank you for your timely reply!
>  I changed the installation direction according to the README document and 
> redirected it to the deal.ii-9.0.1 source code. 
>
 
It seems that you still set the installation directory to a non-existent 
path. If you want to install in your home directory calling

cmake -DCMAKE_INSTALL_PREFIX=${HOME}/deal.II DEAL_II_SOURCE_DIR 


in your build directory should work (you need to replace DEAL_II_SOURCE_DIR 
with the actual path to the deal.II source directory).

Best,
Daniel

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Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread Wolfgang Bangerth 
On 8/11/19 3:49 PM, yuesu jin wrote:
> 
> CMake Error at cmake/scripts/cmake_install.cmake:36 (file):
>    file INSTALL cannot set permissions on
>    "/path/to/install/dir/share/deal.II/scripts/normalize.pl 
> "

What you call cmake initially, you need to replace the string 
"/path/to/install/dir" by the path in which you want to install deal.II. You 
will likely want this to be a directory somewhere under your home directory.

Best
  W.

-- 

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

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Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread yuesu jin 
Hi,all
  I re-installed Deal.II-9.1.1, the message is listed below:
***
Install the project...
-- Install configuration: "DebugRelease"
CMake Error at cmake/scripts/cmake_install.cmake:36 (file):
  file INSTALL cannot set permissions on
  "/path/to/install/dir/share/deal.II/scripts/normalize.pl"
Call Stack (most recent call first):
  cmake_install.cmake:37 (include)



Makefile:61: recipe for target 'install' failed
make: *** [install] Error 1
***
I cannot figure out what is wrong there, can you tell me what is the
problem? Thanks a lot!


On Sat, Aug 10, 2019 at 9:58 PM yuesu jin  wrote:

> Hi, all,
> I am a novice of deal.II, I begun to learn deal.II since version 9.0.1,
> after I updated it from 9.0.1 to 9.1.1, I found the executable file cannot
> run, the message is:
>
>  ./step-5_sec: symbol lookup error: 
> /home/yjin6/anaconda3/lib/libmkl_intel_lp64.so:
> undefined symbol: mkl_blas_dsyrk.
>
> What is the problem? Thanks a lot!
>
> --
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> 
> .
>

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