Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-12 Thread yuesu jin 
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


On Mon, Aug 12, 2019 at 12:12 PM Wolfgang Bangerth 
wrote:

> 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').
>
> Best
>   W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see
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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

2019-08-12 Thread Wolfgang Bangerth 
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').

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

2019-08-12 Thread yuesu jin 
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

On Mon, Aug 12, 2019 at 8:30 AM Wolfgang Bangerth 
wrote:

> 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.
>
> Best
>   W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
> --
> 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

2019-08-12 Thread Wolfgang Bangerth 
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 
> "

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

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 
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!
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see
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> 
> .
>

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