undefined symbol: mkl_blas_dsyrk

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yuesu jin

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Aug 10, 2019, 10:58:53 PM8/10/19
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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!

yuesu jin

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Aug 11, 2019, 5:49:35 PM8/11/19
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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!


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Wolfgang Bangerth

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Aug 11, 2019, 6:00:25 PM8/11/19
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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 <http://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.

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

yuesu jin

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Aug 11, 2019, 6:15:33 PM8/11/19
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Hi, Dr.Bangerth,
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. The compilation cost much time and it output progress message from 0% to 100%. I only copied last few lines because the output is so long. Most of the messages are "building CXX object ............" and "scanning dependencies of target".
**************************************************************************
image.png

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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


Daniel Arndt

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Aug 11, 2019, 6:57:51 PM8/11/19
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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

yuesu jin

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Aug 11, 2019, 8:01:00 PM8/11/19
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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
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Daniel Arndt

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Aug 11, 2019, 10:05:18 PM8/11/19
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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

yuesu jin

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Aug 11, 2019, 10:18:58 PM8/11/19
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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!

yuesu jin

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Aug 11, 2019, 11:08:19 PM8/11/19
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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
#####################################

 

Wolfgang Bangerth

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Aug 12, 2019, 9:30:24 AM8/12/19
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On 8/11/19 9:08 PM, yuesu jin wrote:
> AH... I understand,/*cmake -DCMAKE_INSTALL_PREFIX=[Directory you want to
> install] [Directory you build the program]*/

No, the second [...] block is the directory where the sources are located, not
where you build the program. The directory where you build the program is the
directory you are currently in when you call 'cmake'.


> 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 <http://normalize.pl>"

You still have the /path/to/install/dir/ here. Delete the build directory and
start from scratch.

yuesu jin

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Aug 12, 2019, 1:01:26 PM8/12/19
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Hi Dr.Bangerth,
   Installation completed, what a stupid mistake I made! Appreciate for your support!
   All the problem should be the symbol mkl_blas_dsyrk. It may be caused by my anaconda package manager because the message said:
/step-5_sec: symbol lookup error: /home/yjin6/anaconda3/lib/libmkl_intel_lp64.so: undefined symbol: mkl_blas_dsyrk
   I try to fix it .
Best regards,
Yuesu

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Wolfgang Bangerth

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Aug 12, 2019, 1:12:18 PM8/12/19
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On 8/12/19 11:01 AM, yuesu jin wrote:
>
>    Installation completed, what a stupid mistake I made! Appreciate for
> your support!
> All the problem should be the symbol mkl_blas_dsyrk. It may be caused by
> my anaconda package manager because the message said:
> /*/step-5_sec: symbol lookup error:
> /home/yjin6/anaconda3/lib/libmkl_intel_lp64.so: undefined symbol:
> mkl_blas_dsyrk
> */
>    I try to fix it .

Yuesu,
ok, at least now you're back in business. Linking with the MKL is
difficult. The kind of situation you report is listed on many websites
-- an example is here:

https://software.intel.com/en-us/articles/symbol-lookup-error-when-linking-intel-mkl-with-gcc-on-ubuntu

Can you try the following: on the command line, say
export LD_PRELOAD=/path/to/libmkl_core.so:/path/to/libmkl_intel_thread.so
where you need to replace /path/to by the directory in which the
libmkl_core.so and libmkl_intel_thread.so libraries are located. Then
issue the last of the commands again that led to the error above (I
suspect that that was 'make install').

yuesu jin

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Aug 12, 2019, 4:09:24 PM8/12/19
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Hi Dr.Bangerth,
   I know where is the problem. My bash is in the anaconda environment (with (base) in front of the command line.), so all the library links are referenced to anaconda library. I modified the bashrc scripts then all goes well!! Thanks a lot! I have learned a lesson about linux bash. It really cost my time!
Best regards,
Yuesu
 

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