Re: [deal.II] Trouble getting UMFPACK to work

[Darius Barreto]

Dear Jean-Paul,

Yes,  I was able to solve that problem.  I installed LAPACK using the
command and later I compiled the entire deal.II library. Thanks for the
help.

Regards,

Darius Barreto.

On Wed, Feb 20, 2019 at 2:58 PM Jean-Paul Pelteret 
wrote:

> Dear Darius,
>
> I just thought I’d ask whether you were able to solve your problem?
>
> Best,
> Jean-Paul
>
> On 16 Feb 2019, at 05:22, Darius Barreto  wrote:
>
> Dear Jean-Paul,
>
> Thanks for the reply.
>
>
>
> On Thursday, February 14, 2019 at 9:20:39 PM UTC+5:30, Jean-Paul Pelteret
> wrote:
>>
>> Dear Darius,
>>
>> template 
>> void elastic_rod::solve(){
>> SparseDirectUMFPACK A_direct;
>> A_direct.initialize(system_matrix) ;
>> A_direct.vmult(solution, system_rhs);
>> }
>> Since I am new to dealii, so instead of creating a new  CMakeLists.txt
>> file I have just copied my code in step-29 example(as It uses this
>> UMFPACK), of course I have ensured to change the name in the .txt file. I
>> am getting the error. I have attached the error message.  Do I actually
>> need to make changes( unlike other tutorials) while  entering the cmake
>> command in the terminal?(cmake
>> -DDEAL_II_WITH_DIR=/path/to/installed/deal.II). I have also included the
>> header file for the sparse direct solver UMFPACK(#include
>> ). My other tutorials are just running fine in
>> dealii, except the ones which use an UMFPACK.
>>
>> You suggested me to install an external LAPACK on the group, but I have
>> difficulties in installing it. I was unable to find a proper source in
>> google regarding its installation procedure. So could it be the only reason
>> of not having an external LAPACK?.
>>
>>
>> I’m gathering from the picture that you sent me that the operating system
>> that you’re running is Ubuntu 18.04 or thereabouts. You should be able to
>> install LAPACK with the command “sudo apt install liblapack-dev”. After
>> that, you should *recompile* deal.II itself (not the tutorial example,
>> or your code, but the actual library). It is during the configuration stage
>> for deal.II that UMFPACK is detected and, therefore, enabled within
>> deal.II. It also at this point that you should see the messages that I
>> mentioned earlier, if the detection of UMFPACK was successful. If you’re
>> having trouble installing deal.II itself, then you should consider
>> installing deal.II using candi (https://github.com/dealii/candi) or
>> spack (https://github.com/spack/spack
>> 
>>  / https://github.com/dealii/dealii/wiki/deal.II-in-Spack).
>>
>> I hope that this clarify what you need to do.
>> Best,
>> Jean-Paul
>>
>> On 14 Feb 2019, at 08:16, Jean-Paul Pelteret  wrote:
>>
>> Dear Darius,
>>
>> Your installation of deal.II has not been compiled with UMFPACK supplied
>> as an external library. The bundled version has also not been built, likely
>> because you do not have the required dependencies installed. I believe that
>> you need to have LAPACK installed for it to work, so you should install
>> LAPACK and then try to configure and then build deal.II again. At the end
>> of the configuration step you should see a line similar to this in the
>> summary printed to the console:
>>
>> #DEAL_II_WITH_UMFPACK successfully set up with bundled packages.
>>
>> or
>>
>> #DEAL_II_WITH_UMFPACK set up with external dependencies
>>
>> I hope that this helps you resolve your issue.
>>
>> Best,
>> Jean-Paul
>>
>> On 13 Feb 2019, at 12:38, Darius Barreto  wrote:
>>
>> Hi John,
>>
>> I am exactly getting the same error message?. How were you able to
>> rectify it?.
>> Could you please help?.
>>
>> Thanks
>>
>>
>>
>> On Thursday, August 31, 2017 at 9:28:52 PM UTC+5:30, John wrote:
>>>
>>> Hello everyone,
>>>
>>> I am currently using Deal II version 8.0.0. When I try to run a project
>>> I am getting the following:
>>>
>>> 
>>> Exception on processing:
>>>
>>> 
>>> An error occurred in line <379> of file 
>>> 
>>> in function
>>> void dealii::SparseDirectUMFPACK::factorize(const Matrix&) [with
>>> Matrix = dealii::SparseMatrix]
>>> The violated condition was:
>>> false
>>> The name and call sequence of the exception was:
>>> ExcMessage("To call this function you need UMFPACK, but configured
>>> deal.II without passing the necessary switch to 'cmake'. Please consult the
>>> installation instructions in doc/readme.html.")
>>> Additional Information:
>>> To call this function you need UMFPACK, but configured deal.II without
>>> passing the necessary switch to 'cmake'. Please consult the installation
>>> instructions in doc/readme.html.
>>>
>>> Stacktrace:
>>> ---
>>> #0  /Downloads/deal.II/lib/libdeal_II.so.8.0.0: void
>>> dealii::SparseDirectUMFPACK::factorize
>>> >(dealii::SparseMatrix const&)
>>> #1  step-3: TmsProblem::solve()
>>> #2  step-3: 

Re: [deal.II] Trouble getting UMFPACK to work

[Jean-Paul Pelteret]

Dear Darius,

I just thought I’d ask whether you were able to solve your problem?

Best,
Jean-Paul

> On 16 Feb 2019, at 05:22, Darius Barreto  wrote:
> 
> Dear Jean-Paul,
> 
> Thanks for the reply. 
> 
> 
> 
> On Thursday, February 14, 2019 at 9:20:39 PM UTC+5:30, Jean-Paul Pelteret 
> wrote:
> Dear Darius,
> 
>> template 
>> void elastic_rod::solve(){
>> SparseDirectUMFPACK A_direct;
>>  A_direct.initialize(system_matrix) ;
>>  A_direct.vmult(solution, system_rhs);
>>  }
>> Since I am new to dealii, so instead of creating a new  CMakeLists.txt file 
>> I have just copied my code in step-29 example(as It uses this UMFPACK), of 
>> course I have ensured to change the name in the .txt file. I am getting the 
>> error. I have attached the error message.  Do I actually need to make 
>> changes( unlike other tutorials) while  entering the cmake command in the 
>> terminal?(cmake -DDEAL_II_WITH_DIR=/path/to/installed/deal.II). I have also 
>> included the header file for the sparse direct solver UMFPACK(#include 
>> ). My other tutorials are just running fine in 
>> dealii, except the ones which use an UMFPACK.
>> 
>> You suggested me to install an external LAPACK on the group, but I have 
>> difficulties in installing it. I was unable to find a proper source in 
>> google regarding its installation procedure. So could it be the only reason 
>> of not having an external LAPACK?.
> 
> 
> I’m gathering from the picture that you sent me that the operating system 
> that you’re running is Ubuntu 18.04 or thereabouts. You should be able to 
> install LAPACK with the command “sudo apt install liblapack-dev”. After that, 
> you should recompile deal.II itself (not the tutorial example, or your code, 
> but the actual library). It is during the configuration stage for deal.II 
> that UMFPACK is detected and, therefore, enabled within deal.II. It also at 
> this point that you should see the messages that I mentioned earlier, if the 
> detection of UMFPACK was successful. If you’re having trouble installing 
> deal.II itself, then you should consider installing deal.II using candi 
> (https://github.com/dealii/candi ) or spack 
> (https://github.com/spack/spack 
> 
>  / https://github.com/dealii/dealii/wiki/deal.II-in-Spack 
> ).
> 
> I hope that this clarify what you need to do.
> Best,
> Jean-Paul
> 
>> On 14 Feb 2019, at 08:16, Jean-Paul Pelteret gmail.com 
>> > wrote:
>> 
>> Dear Darius,
>> 
>> Your installation of deal.II has not been compiled with UMFPACK supplied as 
>> an external library. The bundled version has also not been built, likely 
>> because you do not have the required dependencies installed. I believe that 
>> you need to have LAPACK installed for it to work, so you should install 
>> LAPACK and then try to configure and then build deal.II again. At the end of 
>> the configuration step you should see a line similar to this in the summary 
>> printed to the console:
>> 
>> #DEAL_II_WITH_UMFPACK successfully set up with bundled packages.
>> 
>> or
>> 
>> #DEAL_II_WITH_UMFPACK set up with external dependencies
>> 
>> I hope that this helps you resolve your issue.
>> 
>> Best,
>> Jean-Paul
>> 
>>> On 13 Feb 2019, at 12:38, Darius Barreto gmail.com 
>>> > wrote:
>>> 
>>> Hi John,
>>> 
>>> I am exactly getting the same error message?. How were you able to rectify 
>>> it?.
>>> Could you please help?.
>>> 
>>> Thanks
>>> 
>>> 
>>> 
>>> On Thursday, August 31, 2017 at 9:28:52 PM UTC+5:30, John wrote:
>>> Hello everyone,
>>> 
>>> I am currently using Deal II version 8.0.0. When I try to run a project I 
>>> am getting the following:
>>> 
>>> 
>>> Exception on processing: 
>>> 
>>> 
>>> An error occurred in line <379> of file 
>>>  in function
>>> void dealii::SparseDirectUMFPACK::factorize(const Matrix&) [with Matrix 
>>> = dealii::SparseMatrix]
>>> The violated condition was: 
>>> false
>>> The name and call sequence of the exception was:
>>> ExcMessage("To call this function you need UMFPACK, but configured 
>>> deal.II without passing the necessary switch to 'cmake'. Please consult the 
>>> installation instructions in doc/readme.html.")
>>> Additional Information: 
>>> To call this function you need UMFPACK, but configured deal.II without 
>>> passing the necessary switch to 'cmake'. Please consult the installation 
>>> instructions in doc/readme.html.
>>> 
>>> Stacktrace:
>>> ---
>>> #0  /Downloads/deal.II/lib/libdeal_II.so.8.0.0: void 
>>> dealii::SparseDirectUMFPACK::factorize 
>>> >(dealii::SparseMatrix const&)
>>> #1  step-3: TmsProblem::solve()
>>> #2  step-3: TmsProblem::run()
>>> #3  step-3: main
>>> 

Re: [deal.II] Trouble getting UMFPACK to work

[Darius Barreto]

Dear Jean-Paul,

Thanks for the reply. 



On Thursday, February 14, 2019 at 9:20:39 PM UTC+5:30, Jean-Paul Pelteret 
wrote:
>
> Dear Darius,
>
> template 
> void elastic_rod::solve(){
> SparseDirectUMFPACK A_direct;
> A_direct.initialize(system_matrix) ;
> A_direct.vmult(solution, system_rhs);
> }
> Since I am new to dealii, so instead of creating a new  CMakeLists.txt 
> file I have just copied my code in step-29 example(as It uses this 
> UMFPACK), of course I have ensured to change the name in the .txt file. I 
> am getting the error. I have attached the error message.  Do I actually 
> need to make changes( unlike other tutorials) while  entering the cmake 
> command in the terminal?(cmake 
> -DDEAL_II_WITH_DIR=/path/to/installed/deal.II). I have also included the 
> header file for the sparse direct solver UMFPACK(#include 
> ). My other tutorials are just running fine in 
> dealii, except the ones which use an UMFPACK.
>
> You suggested me to install an external LAPACK on the group, but I have 
> difficulties in installing it. I was unable to find a proper source in 
> google regarding its installation procedure. So could it be the only reason 
> of not having an external LAPACK?.
>
>
> I’m gathering from the picture that you sent me that the operating system 
> that you’re running is Ubuntu 18.04 or thereabouts. You should be able to 
> install LAPACK with the command “sudo apt install liblapack-dev”. After 
> that, you should *recompile* deal.II itself (not the tutorial example, or 
> your code, but the actual library). It is during the configuration stage 
> for deal.II that UMFPACK is detected and, therefore, enabled within 
> deal.II. It also at this point that you should see the messages that I 
> mentioned earlier, if the detection of UMFPACK was successful. If you’re 
> having trouble installing deal.II itself, then you should consider 
> installing deal.II using candi (https://github.com/dealii/candi) or spack 
> (https://github.com/spack/spack 
> 
>  / 
> https://github.com/dealii/dealii/wiki/deal.II-in-Spack).
>
> I hope that this clarify what you need to do.
> Best,
> Jean-Paul
>
> On 14 Feb 2019, at 08:16, Jean-Paul Pelteret  > wrote:
>
> Dear Darius,
>
> Your installation of deal.II has not been compiled with UMFPACK supplied 
> as an external library. The bundled version has also not been built, likely 
> because you do not have the required dependencies installed. I believe that 
> you need to have LAPACK installed for it to work, so you should install 
> LAPACK and then try to configure and then build deal.II again. At the end 
> of the configuration step you should see a line similar to this in the 
> summary printed to the console:
>
> #DEAL_II_WITH_UMFPACK successfully set up with bundled packages.
>
> or
>
> #DEAL_II_WITH_UMFPACK set up with external dependencies
>
> I hope that this helps you resolve your issue.
>
> Best,
> Jean-Paul
>
> On 13 Feb 2019, at 12:38, Darius Barreto > 
> wrote:
>
> Hi John,
>
> I am exactly getting the same error message?. How were you able to rectify 
> it?.
> Could you please help?.
>
> Thanks
>
>
>
> On Thursday, August 31, 2017 at 9:28:52 PM UTC+5:30, John wrote:
>>
>> Hello everyone,
>>
>> I am currently using Deal II version 8.0.0. When I try to run a project I 
>> am getting the following:
>>
>> 
>> Exception on processing: 
>>
>> 
>> An error occurred in line <379> of file 
>>  
>> in function
>> void dealii::SparseDirectUMFPACK::factorize(const Matrix&) [with 
>> Matrix = dealii::SparseMatrix]
>> The violated condition was: 
>> false
>> The name and call sequence of the exception was:
>> ExcMessage("To call this function you need UMFPACK, but configured 
>> deal.II without passing the necessary switch to 'cmake'. Please consult the 
>> installation instructions in doc/readme.html.")
>> Additional Information: 
>> To call this function you need UMFPACK, but configured deal.II without 
>> passing the necessary switch to 'cmake'. Please consult the installation 
>> instructions in doc/readme.html.
>>
>> Stacktrace:
>> ---
>> #0  /Downloads/deal.II/lib/libdeal_II.so.8.0.0: void 
>> dealii::SparseDirectUMFPACK::factorize 
>> >(dealii::SparseMatrix const&)
>> #1  step-3: TmsProblem::solve()
>> #2  step-3: TmsProblem::run()
>> #3  step-3: main
>> 
>>
>> Aborting!
>> 
>> CMake Error at CMakeFiles/run_target.cmake:6 (MESSAGE):
>>   
>>
>>   Program terminated with exit code: 1
>>
>>
>> CMakeFiles/run.dir/build.make:57: recipe for target 'CMakeFiles/run' 
>> failed
>> make[3]: *** [CMakeFiles/run] Error 1
>> CMakeFiles/Makefile2:264: recipe for target 'CMakeFiles/run.dir/all' 
>> failed

Re: [deal.II] Trouble getting UMFPACK to work

[Jean-Paul Pelteret]

Dear Darius,

> template 
> void elastic_rod::solve(){
> SparseDirectUMFPACK A_direct;
>   A_direct.initialize(system_matrix) ;
>   A_direct.vmult(solution, system_rhs);
>   }
> Since I am new to dealii, so instead of creating a new  CMakeLists.txt file I 
> have just copied my code in step-29 example(as It uses this UMFPACK), of 
> course I have ensured to change the name in the .txt file. I am getting the 
> error. I have attached the error message.  Do I actually need to make 
> changes( unlike other tutorials) while  entering the cmake command in the 
> terminal?(cmake -DDEAL_II_WITH_DIR=/path/to/installed/deal.II). I have also 
> included the header file for the sparse direct solver UMFPACK(#include 
> ). My other tutorials are just running fine in 
> dealii, except the ones which use an UMFPACK.
> 
> You suggested me to install an external LAPACK on the group, but I have 
> difficulties in installing it. I was unable to find a proper source in google 
> regarding its installation procedure. So could it be the only reason of not 
> having an external LAPACK?.


I’m gathering from the picture that you sent me that the operating system that 
you’re running is Ubuntu 18.04 or thereabouts. You should be able to install 
LAPACK with the command “sudo apt install liblapack-dev”. After that, you 
should recompile deal.II itself (not the tutorial example, or your code, but 
the actual library). It is during the configuration stage for deal.II that 
UMFPACK is detected and, therefore, enabled within deal.II. It also at this 
point that you should see the messages that I mentioned earlier, if the 
detection of UMFPACK was successful. If you’re having trouble installing 
deal.II itself, then you should consider installing deal.II using candi 
(https://github.com/dealii/candi ) or spack 
(https://github.com/spack/spack  / 
https://github.com/dealii/dealii/wiki/deal.II-in-Spack 
).

I hope that this clarify what you need to do.
Best,
Jean-Paul

> On 14 Feb 2019, at 08:16, Jean-Paul Pelteret  wrote:
> 
> Dear Darius,
> 
> Your installation of deal.II has not been compiled with UMFPACK supplied as 
> an external library. The bundled version has also not been built, likely 
> because you do not have the required dependencies installed. I believe that 
> you need to have LAPACK installed for it to work, so you should install 
> LAPACK and then try to configure and then build deal.II again. At the end of 
> the configuration step you should see a line similar to this in the summary 
> printed to the console:
> 
> #DEAL_II_WITH_UMFPACK successfully set up with bundled packages.
> 
> or
> 
> #DEAL_II_WITH_UMFPACK set up with external dependencies
> 
> I hope that this helps you resolve your issue.
> 
> Best,
> Jean-Paul
> 
>> On 13 Feb 2019, at 12:38, Darius Barreto > > wrote:
>> 
>> Hi John,
>> 
>> I am exactly getting the same error message?. How were you able to rectify 
>> it?.
>> Could you please help?.
>> 
>> Thanks
>> 
>> 
>> 
>> On Thursday, August 31, 2017 at 9:28:52 PM UTC+5:30, John wrote:
>> Hello everyone,
>> 
>> I am currently using Deal II version 8.0.0. When I try to run a project I am 
>> getting the following:
>> 
>> 
>> Exception on processing: 
>> 
>> 
>> An error occurred in line <379> of file 
>>  in function
>> void dealii::SparseDirectUMFPACK::factorize(const Matrix&) [with Matrix 
>> = dealii::SparseMatrix]
>> The violated condition was: 
>> false
>> The name and call sequence of the exception was:
>> ExcMessage("To call this function you need UMFPACK, but configured 
>> deal.II without passing the necessary switch to 'cmake'. Please consult the 
>> installation instructions in doc/readme.html.")
>> Additional Information: 
>> To call this function you need UMFPACK, but configured deal.II without 
>> passing the necessary switch to 'cmake'. Please consult the installation 
>> instructions in doc/readme.html.
>> 
>> Stacktrace:
>> ---
>> #0  /Downloads/deal.II/lib/libdeal_II.so.8.0.0: void 
>> dealii::SparseDirectUMFPACK::factorize 
>> >(dealii::SparseMatrix const&)
>> #1  step-3: TmsProblem::solve()
>> #2  step-3: TmsProblem::run()
>> #3  step-3: main
>> 
>> 
>> Aborting!
>> 
>> CMake Error at CMakeFiles/run_target.cmake:6 (MESSAGE):
>>   
>> 
>>   Program terminated with exit code: 1
>> 
>> 
>> CMakeFiles/run.dir/build.make:57: recipe for target 'CMakeFiles/run' failed
>> make[3]: *** [CMakeFiles/run] Error 1
>> CMakeFiles/Makefile2:264: recipe for target 'CMakeFiles/run.dir/all' failed
>> make[2]: *** [CMakeFiles/run.dir/all] Error 2
>> CMakeFiles/Makefile2:271: recipe for 

Re: [deal.II] Trouble getting UMFPACK to work

[Jean-Paul Pelteret]

Dear Darius,

Your installation of deal.II has not been compiled with UMFPACK supplied as an 
external library. The bundled version has also not been built, likely because 
you do not have the required dependencies installed. I believe that you need to 
have LAPACK installed for it to work, so you should install LAPACK and then try 
to configure and then build deal.II again. At the end of the configuration step 
you should see a line similar to this in the summary printed to the console:

#DEAL_II_WITH_UMFPACK successfully set up with bundled packages.

or

#DEAL_II_WITH_UMFPACK set up with external dependencies

I hope that this helps you resolve your issue.

Best,
Jean-Paul

> On 13 Feb 2019, at 12:38, Darius Barreto  wrote:
> 
> Hi John,
> 
> I am exactly getting the same error message?. How were you able to rectify 
> it?.
> Could you please help?.
> 
> Thanks
> 
> 
> 
> On Thursday, August 31, 2017 at 9:28:52 PM UTC+5:30, John wrote:
> Hello everyone,
> 
> I am currently using Deal II version 8.0.0. When I try to run a project I am 
> getting the following:
> 
> 
> Exception on processing: 
> 
> 
> An error occurred in line <379> of file 
>  in function
> void dealii::SparseDirectUMFPACK::factorize(const Matrix&) [with Matrix = 
> dealii::SparseMatrix]
> The violated condition was: 
> false
> The name and call sequence of the exception was:
> ExcMessage("To call this function you need UMFPACK, but configured 
> deal.II without passing the necessary switch to 'cmake'. Please consult the 
> installation instructions in doc/readme.html.")
> Additional Information: 
> To call this function you need UMFPACK, but configured deal.II without 
> passing the necessary switch to 'cmake'. Please consult the installation 
> instructions in doc/readme.html.
> 
> Stacktrace:
> ---
> #0  /Downloads/deal.II/lib/libdeal_II.so.8.0.0: void 
> dealii::SparseDirectUMFPACK::factorize 
> >(dealii::SparseMatrix const&)
> #1  step-3: TmsProblem::solve()
> #2  step-3: TmsProblem::run()
> #3  step-3: main
> 
> 
> Aborting!
> 
> CMake Error at CMakeFiles/run_target.cmake:6 (MESSAGE):
>   
> 
>   Program terminated with exit code: 1
> 
> 
> CMakeFiles/run.dir/build.make:57: recipe for target 'CMakeFiles/run' failed
> make[3]: *** [CMakeFiles/run] Error 1
> CMakeFiles/Makefile2:264: recipe for target 'CMakeFiles/run.dir/all' failed
> make[2]: *** [CMakeFiles/run.dir/all] Error 2
> CMakeFiles/Makefile2:271: recipe for target 'CMakeFiles/run.dir/rule' failed
> make[1]: *** [CMakeFiles/run.dir/rule] Error 2
> Makefile:196: recipe for target 'run' failed
> make: *** [run] Error 2
> 
> 
> 
> I have tried "cmake -DDEAL_II_WITH_UMFPACK=ON" and "cmake 
> -DDEAL_II_WITH_UMFPACK=ON -DUMFPACK_DIR=/Downloads/deal.II/bundled/umfpack ." 
> and also  "cmake -DDEAL_II_WITH_UMFPACK=ON 
> -DUMFPACK_DIR=/Downloads/deal.II/bundled/umfpack/UMFPACK ." and then 
> following each of these with "make" and "make run". However, all of these 
> still end up giving me the same error as above. Can anyone help me with 
> getting umfpack to work? Thank you in advance.
> 
> -- 
> 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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> .
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> .

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Re: [deal.II] Trouble getting UMFPACK to work

[Bruno Turcksin]

2017-09-12 9:49 GMT-04:00 曾元圆 <2012zg...@gmail.com>:

> If I want to run all the 57 steps, should I install all the mentioned
> libraries? How can I know in advance which library I may need? Perhaps now
> I don't need PETSc, but maybe someday in the future I will need.
>
No you don't. You can use candi  or spack
 to install
everything and then, you won't have to worry about missing a library.

Best,

Bruno

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Re: [deal.II] Trouble getting UMFPACK to work

[曾元圆]

If I want to run all the 57 steps, should I install all the mentioned 
libraries? How can I know in advance which library I may need? Perhaps now 
I don't need PETSc, but maybe someday in the future I will need. 

在 2017年9月12日星期二 UTC+8下午8:08:14，Bruno Turcksin写道：
>
> 2017-09-11 23:45 GMT-04:00 曾元圆 <2012...@gmail.com >:
> >  Thank you very much! So you mean every time I want to use another 
> library,
> > I have to recompile and reinstall dealii again?
> Every time you add a new library you need to *reconfigure* and recompile 
> deal. Now if you want to use PETSc and Trilinos you can turn on both of 
> them at the same time. You don't need to recompile deal twice. Ideally, the 
> first time you configure deal, you would turn on the support for the all 
> libraries that you will need. This way you only have to compile deal.II 
> once.
>
> Best,
>
> Bruno
>

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Re: [deal.II] Trouble getting UMFPACK to work

[Bruno Turcksin]

2017-09-11 23:45 GMT-04:00 曾元圆 <2012zg...@gmail.com>:
>  Thank you very much! So you mean every time I want to use another
library,
> I have to recompile and reinstall dealii again?
Every time you add a new library you need to *reconfigure* and recompile
deal. Now if you want to use PETSc and Trilinos you can turn on both of
them at the same time. You don't need to recompile deal twice. Ideally, the
first time you configure deal, you would turn on the support for the all
libraries that you will need. This way you only have to compile deal.II
once.

Best,

Bruno

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Re: [deal.II] Trouble getting UMFPACK to work

[曾元圆]

 Thank you very much! So you mean every time I want to use another library, 
I have to recompile and reinstall dealii again?

在 2017年9月12日星期二 UTC+8上午1:25:25，Bruno Turcksin写道：
>
> 2017-09-11 13:11 GMT-04:00 曾元圆 <2012...@gmail.com >: 
> > Because I have already installed dealii, I don't quite understand what 
> you 
> > mean by saying "configuring". Do you mean I need to recompile the whole 
> > dealii then it can know where to find lapack?  LAPACK is a third party 
> > library right? so all I need to do is to tell the compiler where is the 
> > header and library. I suppose perhaps I don't need to configure dealii 
> > again?  sorry I really don't know much about cmake. Forgive me if I 
> asked 
> > you some silly questions. 
> To install deal.II, you have basically two steps: 1) the configuration 
> (that's when you use cmake and give all the options that you want for 
> example -DDEAL_II_WITH_UMFPACK=ON) 2) the compilation itself. 
> In step 1, all the compiler commands are generated and they are 
> executed during step 2. Like you correctly said, you need to tell the 
> compiler where the header and the library are, this is done during 
> step 1. However, this is slightly more complicated that just giving a 
> path, because some part of deal.II are only activated if some 
> libraries are present. For example, if you are using UMFPACK some 
> files will need to be compiled but if you are not using UMFPACK they 
> won't be compiled. So having deal.II compiled without UMFPACK support 
> and then, adding the flags to the library won't work because the files 
> that allow to use UMFPACK from deal.II won't be compiled. Basically 
> deal.II would not be aware that UMDPACK is installed. So what you need 
> to do is to reinstall deal.II from the very beginning in a new 
> directory. 
> Does it make sense? 
>
> Best, 
>
> Bruno 
>

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Re: [deal.II] Trouble getting UMFPACK to work

[Bruno Turcksin]

2017-09-11 13:11 GMT-04:00 曾元圆 <2012zg...@gmail.com>:
> Because I have already installed dealii, I don't quite understand what you
> mean by saying "configuring". Do you mean I need to recompile the whole
> dealii then it can know where to find lapack?  LAPACK is a third party
> library right? so all I need to do is to tell the compiler where is the
> header and library. I suppose perhaps I don't need to configure dealii
> again?  sorry I really don't know much about cmake. Forgive me if I asked
> you some silly questions.
To install deal.II, you have basically two steps: 1) the configuration
(that's when you use cmake and give all the options that you want for
example -DDEAL_II_WITH_UMFPACK=ON) 2) the compilation itself.
In step 1, all the compiler commands are generated and they are
executed during step 2. Like you correctly said, you need to tell the
compiler where the header and the library are, this is done during
step 1. However, this is slightly more complicated that just giving a
path, because some part of deal.II are only activated if some
libraries are present. For example, if you are using UMFPACK some
files will need to be compiled but if you are not using UMFPACK they
won't be compiled. So having deal.II compiled without UMFPACK support
and then, adding the flags to the library won't work because the files
that allow to use UMFPACK from deal.II won't be compiled. Basically
deal.II would not be aware that UMDPACK is installed. So what you need
to do is to reinstall deal.II from the very beginning in a new
directory.
Does it make sense?

Best,

Bruno

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Re: [deal.II] Trouble getting UMFPACK to work

[曾元圆]

Because I have already installed dealii, I don't quite understand what you 
mean by saying "configuring". Do you mean I need to recompile the whole 
dealii then it can know where to find lapack?  LAPACK is a third party 
library right? so all I need to do is to tell the compiler where is the 
header and library. I suppose perhaps I don't need to configure dealii 
again?  sorry I really don't know much about cmake. Forgive me if I asked 
you some silly questions. 

best regards.

在 2017年9月11日星期一 UTC+8下午8:22:11，Bruno Turcksin写道：
>
> 2017-09-11 0:30 GMT-04:00 曾元圆 <2012...@gmail.com >: 
> > So UMFPACK is not installed, right? But what to do next?  How can I know 
> > whether my Ubuntu OS already installed the lapack and blas package? 
> No UMFPACK has not been installed and lapack has not been found. You 
> need to install the dev version of lapack otherwise the headers are 
> not installed. Without the headers, lapack cannot be used by deal. So 
> make sure you get ( DEAL_II_WITH_LAPACK = ON ) You can also add 
> -DDEAL_II_WITH_LAPACK=ON when configuring deal.II and cmake will let 
> you know if there is a problem. 
>
> > I can intall lapack and blas myself, but I don't know how to compile and 
> > install UMFPACK. 
> You don't need to install UMFPACK yourself. It will be installed by 
> deal.II. 
>
> Best, 
>
> Bruno 
>

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Re: [deal.II] Trouble getting UMFPACK to work

[曾元圆]

Now suppose I have installed blas and lapack by execute command in 
terminal. Then the remaining part is UMPACK. Since "DEAL_II_WITH_UMFPACK = 
OFF" is apparently not expected. What I want to know is what I should do to 
change it to  " DEAL_II_WITH_UMFPACK set up with bundled packages", which 
is what we want.


在 2017年9月11日星期一 UTC+8下午8:22:11，Bruno Turcksin写道：
>
> 2017-09-11 0:30 GMT-04:00 曾元圆 <2012...@gmail.com >: 
> > So UMFPACK is not installed, right? But what to do next?  How can I know 
> > whether my Ubuntu OS already installed the lapack and blas package? 
> No UMFPACK has not been installed and lapack has not been found. You 
> need to install the dev version of lapack otherwise the headers are 
> not installed. Without the headers, lapack cannot be used by deal. So 
> make sure you get ( DEAL_II_WITH_LAPACK = ON ) You can also add 
> -DDEAL_II_WITH_LAPACK=ON when configuring deal.II and cmake will let 
> you know if there is a problem. 
>
> > I can intall lapack and blas myself, but I don't know how to compile and 
> > install UMFPACK. 
> You don't need to install UMFPACK yourself. It will be installed by 
> deal.II. 
>
> Best, 
>
> Bruno 
>

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Re: [deal.II] Trouble getting UMFPACK to work

[Wolfgang Bangerth]

On 09/11/2017 10:40 AM, 曾元圆 wrote:

thank you but, nothing need to do with UMFPACK?


No -- deal.II has its own copy of UMFPACK. So, whenever deal.II can find 
BLAS and LAPACK, it uses its own copy of UMFPACK. (It uses a copy of 
UMFPACK if one is found on your system, but because it has its own copy, 
it doesn't *need* to find one installed on the system.)


Best
 W.

--

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   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Trouble getting UMFPACK to work

[曾元圆]

more specifically？

在 2017年9月11日星期一 UTC+8下午8:22:11，Bruno Turcksin写道：
>
> 2017-09-11 0:30 GMT-04:00 曾元圆 <2012...@gmail.com >: 
> > So UMFPACK is not installed, right? But what to do next?  How can I know 
> > whether my Ubuntu OS already installed the lapack and blas package? 
> No UMFPACK has not been installed and lapack has not been found. You 
> need to install the dev version of lapack otherwise the headers are 
> not installed. Without the headers, lapack cannot be used by deal. So 
> make sure you get ( DEAL_II_WITH_LAPACK = ON ) You can also add 
> -DDEAL_II_WITH_LAPACK=ON when configuring deal.II and cmake will let 
> you know if there is a problem. 
>
> > I can intall lapack and blas myself, but I don't know how to compile and 
> > install UMFPACK. 
> You don't need to install UMFPACK yourself. It will be installed by 
> deal.II. 
>
> Best, 
>
> Bruno 
>

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Re: [deal.II] Trouble getting UMFPACK to work

[Bruno Turcksin]

2017-09-11 0:30 GMT-04:00 曾元圆 <2012zg...@gmail.com>:
> So UMFPACK is not installed, right? But what to do next?  How can I know
> whether my Ubuntu OS already installed the lapack and blas package?
No UMFPACK has not been installed and lapack has not been found. You
need to install the dev version of lapack otherwise the headers are
not installed. Without the headers, lapack cannot be used by deal. So
make sure you get ( DEAL_II_WITH_LAPACK = ON ) You can also add
-DDEAL_II_WITH_LAPACK=ON when configuring deal.II and cmake will let
you know if there is a problem.

> I can intall lapack and blas myself, but I don't know how to compile and
> install UMFPACK.
You don't need to install UMFPACK yourself. It will be installed by deal.II.

Best,

Bruno

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Re: [deal.II] Trouble getting UMFPACK to work

[John]

Wolfgang, you are absolutely correct. My mistake was not having BLAS and 
LAPACK, so it was unable to use UMFPACK. Thank you for all of your help!






On Monday, September 4, 2017 at 7:29:01 PM UTC-4, Wolfgang Bangerth wrote:
>
> On 09/02/2017 08:54 AM, 曾元圆 wrote: 
> > have you solve this problem? I encountered the same problem as you. 
> Actually 
> > I'm following an FEM open course on coursera and I'm trying to compile 
> the 
> > source code in the homework. I have installed the dealii just a few days 
> ago 
> > so I don't think it has something to do with the version of dealii. 
> > 
> > 在 2017年9月1日星期五 UTC+8上午3:52:44，John写道： 
> > 
> >   Timo, 
> > 
> > I do eventually plan on updating the code to the latest release. 
> > I was doing the commands inside a folder in deal.II (similar to if I 
> was 
> > in deal.II/examples/step-1). I already have deal.II installed and 
> > compiled. I have been going through a few of the examples perfectly 
> fine. 
> > Should I be trying to run the commands elsewhere? Everything else in 
> the 
> > code has been running just fine until it reaches the point it needs 
> > UMFPACK. Thank you for responding. 
>
> As a general rule, there is no need to compile deal.II and then try to run 
> any 
> programs with it if you want to find out whether your UMFPACK will work or 
> not. All you need to do is to run the 
>cmake  
> command you run to configure deal.II. At the end, it prints out a summary 
> that 
> shows what packages it found. if UMFPACK is not listed as ON, then 
> compiling 
> deal.II to test it is not necessary -- UMFPACK has not been enabled. 
>
> Now, if you do find that UMFPACK has not been enabled, even though you 
> specificed 
>-DDEAL_II_WITH_UMFPACK=ON 
> then you need to go higher up in the cmake output to find what precisely 
> it 
> was that cmake couldn't figure out. The usual cause is that UMFPACK 
> requires 
> BLAS and LAPACK, and if your system does not have these libraries 
> available, 
> or has them in places where cmake can't find them, then UMFPACK can not be 
> enabled. 
>
> What it is in your case that doesn't work, I don't know of course. But you 
> can 
> find out by looking through the cmake output. 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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Re: [deal.II] Trouble getting UMFPACK to work

[John]

I've actually deleted deal.II version 8.0.0 since last writing. I got 
UMFPACK to work by installing BLAS and LAPACK, but then I kept getting an 
error that it was unable to find the MPI library even though I had just 
installed openmpi. Since I could not find a way around this, I ended up 
updating the code to deal.II version 8.1.0, which it is currently running 
successfully on, and am now working on updating to 8.5. Thank you for all 
of your help!




On Monday, September 4, 2017 at 6:35:07 PM UTC-4, Bruno Turcksin wrote:
>
> John, 
>
> 2017-09-02 11:07 GMT-04:00 John : 
> > I still have yet to resolve the issue. As suggested, I have been trying 
> to 
> > delete deal.II and then reinstalling and configuring with 
> > -DDEAL_II_WITH_UMFPACK=ON, but am still having trouble with it. I will 
> write 
> > back to you if/when I figure it out! 
> Please send the detailed.log file and the error message. 
>
> Best, 
>
> Bruno 
>

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Re: [deal.II] Trouble getting UMFPACK to work

[Wolfgang Bangerth]

On 09/02/2017 08:54 AM, 曾元圆 wrote:
have you solve this problem? I encountered the same problem as you. Actually 
I'm following an FEM open course on coursera and I'm trying to compile the 
source code in the homework. I have installed the dealii just a few days ago 
so I don't think it has something to do with the version of dealii.


在 2017年9月1日星期五 UTC+8上午3:52:44，John写道：

  Timo,

I do eventually plan on updating the code to the latest release.
I was doing the commands inside a folder in deal.II (similar to if I was
in deal.II/examples/step-1). I already have deal.II installed and
compiled. I have been going through a few of the examples perfectly fine.
Should I be trying to run the commands elsewhere? Everything else in the
code has been running just fine until it reaches the point it needs
UMFPACK. Thank you for responding.


As a general rule, there is no need to compile deal.II and then try to run any 
programs with it if you want to find out whether your UMFPACK will work or 
not. All you need to do is to run the

  cmake 
command you run to configure deal.II. At the end, it prints out a summary that 
shows what packages it found. if UMFPACK is not listed as ON, then compiling 
deal.II to test it is not necessary -- UMFPACK has not been enabled.


Now, if you do find that UMFPACK has not been enabled, even though you 
specificed
  -DDEAL_II_WITH_UMFPACK=ON
then you need to go higher up in the cmake output to find what precisely it 
was that cmake couldn't figure out. The usual cause is that UMFPACK requires 
BLAS and LAPACK, and if your system does not have these libraries available, 
or has them in places where cmake can't find them, then UMFPACK can not be 
enabled.


What it is in your case that doesn't work, I don't know of course. But you can 
find out by looking through the cmake output.


Best
 W.

--

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

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Re: [deal.II] Trouble getting UMFPACK to work

[Bruno Turcksin]

John,

2017-09-02 11:07 GMT-04:00 John :
> I still have yet to resolve the issue. As suggested, I have been trying to
> delete deal.II and then reinstalling and configuring with
> -DDEAL_II_WITH_UMFPACK=ON, but am still having trouble with it. I will write
> back to you if/when I figure it out!
Please send the detailed.log file and the error message.

Best,

Bruno

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Re: [deal.II] Trouble getting UMFPACK to work

[John]

I still have yet to resolve the issue. As suggested, I have been trying to 
delete deal.II and then reinstalling and configuring with 
-DDEAL_II_WITH_UMFPACK=ON, but am still having trouble with it. I will 
write back to you if/when I figure it out!

On Saturday, September 2, 2017 at 10:54:26 AM UTC-4, 曾元圆 wrote:
>
> hi John,
> have you solve this problem? I encountered the same problem as you. 
> Actually I'm following an FEM open course on coursera and I'm trying to 
> compile the source code in the homework. I have installed the dealii just a 
> few days ago so I don't think it has something to do with the version of 
> dealii.
>
> 在 2017年9月1日星期五 UTC+8上午3:52:44，John写道：
>>
>>  Timo, 
>>
>> I do eventually plan on updating the code to the latest release.
>> I was doing the commands inside a folder in deal.II (similar to if I was 
>> in deal.II/examples/step-1). I already have deal.II installed and compiled. 
>> I have been going through a few of the examples perfectly fine. Should I be 
>> trying to run the commands elsewhere? Everything else in the code has been 
>> running just fine until it reaches the point it needs UMFPACK. Thank you 
>> for responding.
>>
>

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Re: [deal.II] Trouble getting UMFPACK to work

[曾元圆]

hi John,
have you solve this problem? I encountered the same problem as you. 
Actually I'm following an FEM open course on coursera and I'm trying to 
compile the source code in the homework. I have installed the dealii just a 
few days ago so I don't think it has something to do with the version of 
dealii.

在 2017年9月1日星期五 UTC+8上午3:52:44，John写道：
>
>  Timo, 
>
> I do eventually plan on updating the code to the latest release.
> I was doing the commands inside a folder in deal.II (similar to if I was 
> in deal.II/examples/step-1). I already have deal.II installed and compiled. 
> I have been going through a few of the examples perfectly fine. Should I be 
> trying to run the commands elsewhere? Everything else in the code has been 
> running just fine until it reaches the point it needs UMFPACK. Thank you 
> for responding.
>

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Re: [deal.II] Trouble getting UMFPACK to work

[John]

 Timo, 

I do eventually plan on updating the code to the latest release.
I was doing the commands inside a folder in deal.II (similar to if I was in 
deal.II/examples/step-1). I already have deal.II installed and compiled. I 
have been going through a few of the examples perfectly fine. Should I be 
trying to run the commands elsewhere? Everything else in the code has been 
running just fine until it reaches the point it needs UMFPACK. Thank you 
for responding.

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Re: [deal.II] Trouble getting UMFPACK to work

[Timo Heister]

John,

> I am currently using Deal II version 8.0.0.

I would like to encourage you to update to the latest release. Many
things have changed and improved over the years. That probably also
includes handling of dependencies like UMFPACK.

> I have tried "cmake -DDEAL_II_WITH_UMFPACK=ON" and "cmake
> -DDEAL_II_WITH_UMFPACK=ON -DUMFPACK_DIR=/Downloads/deal.II/bundled/umfpack
> ." and also  "cmake -DDEAL_II_WITH_UMFPACK=ON
> -DUMFPACK_DIR=/Downloads/deal.II/bundled/umfpack/UMFPACK ." and then
> following each of these with "make" and "make run".

Just to be sure: you did this in your deal.II build directory and you
then compiled and installed deal.II, right? (using "make install")
Please be sure that no other errors were reported in between.

-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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[deal.II] Trouble getting UMFPACK to work

[John]

Hello everyone,

I am currently using Deal II version 8.0.0. When I try to run a project I 
am getting the following:


Exception on processing: 


An error occurred in line <379> of file 
 
in function
void dealii::SparseDirectUMFPACK::factorize(const Matrix&) [with Matrix 
= dealii::SparseMatrix]
The violated condition was: 
false
The name and call sequence of the exception was:
ExcMessage("To call this function you need UMFPACK, but configured 
deal.II without passing the necessary switch to 'cmake'. Please consult the 
installation instructions in doc/readme.html.")
Additional Information: 
To call this function you need UMFPACK, but configured deal.II without 
passing the necessary switch to 'cmake'. Please consult the installation 
instructions in doc/readme.html.

Stacktrace:
---
#0  /Downloads/deal.II/lib/libdeal_II.so.8.0.0: void 
dealii::SparseDirectUMFPACK::factorize(dealii::SparseMatrix const&)
#1  step-3: TmsProblem::solve()
#2  step-3: TmsProblem::run()
#3  step-3: main


Aborting!

CMake Error at CMakeFiles/run_target.cmake:6 (MESSAGE):
  

  Program terminated with exit code: 1


CMakeFiles/run.dir/build.make:57: recipe for target 'CMakeFiles/run' failed
make[3]: *** [CMakeFiles/run] Error 1
CMakeFiles/Makefile2:264: recipe for target 'CMakeFiles/run.dir/all' failed
make[2]: *** [CMakeFiles/run.dir/all] Error 2
CMakeFiles/Makefile2:271: recipe for target 'CMakeFiles/run.dir/rule' failed
make[1]: *** [CMakeFiles/run.dir/rule] Error 2
Makefile:196: recipe for target 'run' failed
make: *** [run] Error 2



I have tried "*cmake -DDEAL_II_WITH_UMFPACK=ON*" and "*cmake 
-DDEAL_II_WITH_UMFPACK=ON -DUMFPACK_DIR=/Downloads/deal.II/bundled/umfpack 
.*" and also  "*cmake -DDEAL_II_WITH_UMFPACK=ON 
-DUMFPACK_DIR=/Downloads/deal.II/bundled/umfpack/UMFPACK .*" and then 
following each of these with "*make*" and "*make run*". However, all of 
these still end up giving me the same error as above. Can anyone help me 
with getting umfpack to work? Thank you in advance.

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