[deal.II] Installation error of deal.II in the Stampede2 cluster

[David Montiel Taboada]

Hello, 

I am trying to install deal.II v 9.2.0 on the TACC Stampede2 cluster. I 
already a working installation but when I tried to install it again using 
the same instructions I am getting the following error:

/opt/apps/gcc/6.3.0/bin/ld.gold: error: ../lib/libdeal_II.so.9.2.0: bad 
symbol name offset 154807354 at 0

collect2: error: ld returned 1 exit status

make[2]: *** [bin/step-52.release] Error 1

make[1]: *** [examples/CMakeFiles/step-52.release.dir/all] Error 2

make[1]: *** Waiting for unfinished jobs

Here are the cmake and make command lines i used:

$ cmake -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_P4EST=ON 
-DCMAKE_INSTALL_PREFIX=$WORK/dealii_install_2 $WORK/dealii-9.2.0

$ make -j 16 install 

I already tried switching the default intel module by gcc and using a 
previous version of cmake (3.20.2)

I would appreciate any help. 

Best, 

David







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Re: [deal.II] deal.II Installation Error

[Pushkar Pandit]

Dear Dr. Wolgang Bangerth

Certainly that is the case as you illustrated since I am installing deal.II
9.0.0 in order to run PRISMS-PF and my Trilinos is not built with MueLu
which was creating an issue so I excluded the installation with trilinos
during the installation of deal.II and managed to successfully install in
with an error in one of the mpi.cc file where in " MPI_Type_struct(2,
lengths, displacements, types, &type); " line has deprecated MPI function
which I replaced with a newer alternative of this function that
transitioned the successful installation process

Moreover,I am thankful for the quick reply on my query and I would be glad
if my above observations prove to be of any relevance in the development of
library.

Thankfully
Pushkar Anirudha Pandit

On Sat, Apr 3, 2021 at 4:20 AM Wolfgang Bangerth 
wrote:

> On 4/2/21 4:29 AM, pushkar...@gmail.com wrote:
> >
> > /home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc:
> fatal
> > error: MueLu_EpetraOperator.hpp: No such file or directory
> > 34 | #  include 
>
> Pushkar -- the questions to ask are (i) does this file exist, (ii) if it
> does,
> why is the compiler not finding it, (iii) if it does not exist, why not?
>
> MueLu is a part of the Trilinos software. It is conceivable that it was
> part
> of previous Trilinos versions, but is no longer. The current deal.II
> version
> no longer #includes this file, which suggests that indeed that file has
> gone
> away. So we would have fixed this in newer deal.II versions, and one of
> the
> possibilities is that you happen to have an old deal.II but new Trilinos
> version and that these are just no longer compatible. If that is so, you
> will
> have to either upgrade to a newer deal.II version or downgrade Trilinos to
> an
> older version.
>
> 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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> .
>

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Re: [deal.II] deal.II Installation Error

[Wolfgang Bangerth]

On 4/2/21 4:29 AM, pushkar...@gmail.com wrote:


/home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc: fatal 
error: MueLu_EpetraOperator.hpp: No such file or directory

    34 | #  include 


Pushkar -- the questions to ask are (i) does this file exist, (ii) if it does, 
why is the compiler not finding it, (iii) if it does not exist, why not?


MueLu is a part of the Trilinos software. It is conceivable that it was part 
of previous Trilinos versions, but is no longer. The current deal.II version 
no longer #includes this file, which suggests that indeed that file has gone 
away. So we would have fixed this in newer deal.II versions, and one of the 
possibilities is that you happen to have an old deal.II but new Trilinos 
version and that these are just no longer compatible. If that is so, you will 
have to either upgrade to a newer deal.II version or downgrade Trilinos to an 
older version.


Best
 W.

--

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

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[deal.II] Re: deal.II Installation Error

[pushkar...@gmail.com]

Any help in this regard will be helpful .

Regards 
Pushkar

On Friday, April 2, 2021 at 3:59:45 PM UTC+5:30 pushkar...@gmail.com wrote:

>
> Dear deal.II community,
>
> In my attempt to install deal.II with p4est and mpi which I need to run 
> PRISMS-PF I reinstalled the library but faced an error while installation 
> at 50% described as :
>
> /home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc: 
> fatal error: MueLu_EpetraOperator.hpp: No such file or directory
>34 | #  include 
>   |^~
> compilation terminated.
> make[2]: *** [source/lac/CMakeFiles/obj_lac_release.dir/build.make:776: 
> source/lac/CMakeFiles/obj_lac_release.dir/trilinos_precondition_muelu.cc.o] 
> Error 1
> make[1]: *** [CMakeFiles/Makefile2:3445: 
> source/lac/CMakeFiles/obj_lac_release.dir/all] Error 2
> make: *** [Makefile:136: all] Error 2
>
> In this regard any help will be beneficial as in one of the github closed 
> I found that by commenting out this header file one can surpass this issue 
> but when I did that I got another error at 50%  in the same file as: 
>
> /home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc: In 
> member function ‘void 
> dealii::TrilinosWrappers::PreconditionAMGMueLu::initialize(const 
> Epetra_CrsMatrix&, Teuchos::ParameterList&)’:
> /home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc:219:24: 
> error: expected type-specifier
>   219 |   Teuchos::rcp(new Xpetra::EpetraCrsMatrix (rcp_matrix));
>   |^~
> /home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc:233:46: 
> error: ‘EpetraOperator’ is not a member of ‘MueLu’
>   233 | preconditioner = 
> std::make_shared(hierarchy);
>   |  ^~
> /home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc:233:71: 
> error: no matching function for call to ‘make_shared< 
> >(Teuchos::RCP Kokkos::Compat::KokkosDeviceWrapperNode > >&)’
>   233 | preconditioner = 
> std::make_shared(hierarchy);
>   
> |   ^
> In file included from /usr/include/c++/9/memory:81,
>  from 
> /usr/lib/Trilinos/include/Sacado_Fad_Exp_ViewStorage.hpp:35,
>  from 
> /usr/lib/Trilinos/include/Sacado_Fad_Exp_ViewFad.hpp:34,
>  from /usr/lib/Trilinos/include/Sacado.hpp:85,
>  from 
> /home/pushkar/dealii-9.0.0/include/deal.II/base/numbers.h:53,
>  from 
> /home/pushkar/dealii-9.0.0/build/include/deal.II/base/config.h:412,
>  from 
> /home/pushkar/dealii-9.0.0/include/deal.II/lac/trilinos_index_access.h:19,
>  from 
> /home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc:16:
> /usr/include/c++/9/bits/shared_ptr.h:714:5: note: candidate: 
> ‘template std::shared_ptr<_Tp> 
> std::make_shared(_Args&& ...)’
>   714 | make_shared(_Args&&... __args)
>   | ^~~
> /usr/include/c++/9/bits/shared_ptr.h:714:5: note:   template argument 
> deduction/substitution failed:
> /home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc:233:71: 
> error: template argument 1 is invalid
>   233 | preconditioner = 
> std::make_shared(hierarchy);
>   
> |   ^
> make[2]: *** [source/lac/CMakeFiles/obj_lac_release.dir/build.make:776: 
> source/lac/CMakeFiles/obj_lac_release.dir/trilinos_precondition_muelu.cc.o] 
> Error 1
> make[1]: *** [CMakeFiles/Makefile2:3445: 
> source/lac/CMakeFiles/obj_lac_release.dir/all] Error 2
> make: *** [Makefile:136: all] Error 2
>
>

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[deal.II] deal.II Installation Error

[pushkar...@gmail.com]

Dear deal.II community,

In my attempt to install deal.II with p4est and mpi which I need to run 
PRISMS-PF I reinstalled the library but faced an error while installation 
at 50% described as :

/home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc: fatal 
error: MueLu_EpetraOperator.hpp: No such file or directory
   34 | #  include 
  |^~
compilation terminated.
make[2]: *** [source/lac/CMakeFiles/obj_lac_release.dir/build.make:776: 
source/lac/CMakeFiles/obj_lac_release.dir/trilinos_precondition_muelu.cc.o] 
Error 1
make[1]: *** [CMakeFiles/Makefile2:3445: 
source/lac/CMakeFiles/obj_lac_release.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

In this regard any help will be beneficial as in one of the github closed I 
found that by commenting out this header file one can surpass this issue 
but when I did that I got another error at 50%  in the same file as: 

/home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc: In 
member function ‘void 
dealii::TrilinosWrappers::PreconditionAMGMueLu::initialize(const 
Epetra_CrsMatrix&, Teuchos::ParameterList&)’:
/home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc:219:24: 
error: expected type-specifier
  219 |   Teuchos::rcp(new Xpetra::EpetraCrsMatrix (rcp_matrix));
  |^~
/home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc:233:46: 
error: ‘EpetraOperator’ is not a member of ‘MueLu’
  233 | preconditioner = 
std::make_shared(hierarchy);
  |  ^~
/home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc:233:71: 
error: no matching function for call to ‘make_shared< 
>(Teuchos::RCP > >&)’
  233 | preconditioner = 
std::make_shared(hierarchy);
  
|   ^
In file included from /usr/include/c++/9/memory:81,
 from 
/usr/lib/Trilinos/include/Sacado_Fad_Exp_ViewStorage.hpp:35,
 from 
/usr/lib/Trilinos/include/Sacado_Fad_Exp_ViewFad.hpp:34,
 from /usr/lib/Trilinos/include/Sacado.hpp:85,
 from 
/home/pushkar/dealii-9.0.0/include/deal.II/base/numbers.h:53,
 from 
/home/pushkar/dealii-9.0.0/build/include/deal.II/base/config.h:412,
 from 
/home/pushkar/dealii-9.0.0/include/deal.II/lac/trilinos_index_access.h:19,
 from 
/home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc:16:
/usr/include/c++/9/bits/shared_ptr.h:714:5: note: candidate: 
‘template std::shared_ptr<_Tp> 
std::make_shared(_Args&& ...)’
  714 | make_shared(_Args&&... __args)
  | ^~~
/usr/include/c++/9/bits/shared_ptr.h:714:5: note:   template argument 
deduction/substitution failed:
/home/pushkar/dealii-9.0.0/source/lac/trilinos_precondition_muelu.cc:233:71: 
error: template argument 1 is invalid
  233 | preconditioner = 
std::make_shared(hierarchy);
  
|   ^
make[2]: *** [source/lac/CMakeFiles/obj_lac_release.dir/build.make:776: 
source/lac/CMakeFiles/obj_lac_release.dir/trilinos_precondition_muelu.cc.o] 
Error 1
make[1]: *** [CMakeFiles/Makefile2:3445: 
source/lac/CMakeFiles/obj_lac_release.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

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Re: [deal.II] Re: DEAL.II INSTALLATION ERROR

[Pushkar Pandit]

 Marc

I did resolve the above issue as there was some problems with permissions
while installing PETSC and I was installing it with root in /usr/lib/
directory which I installed without root privileges in /home/username/
directory and I did manage to compile the deal.II library with
cmake.Anyways I am grateful to your quick response on my query .

Regards
Pushkar

On Fri, Nov 27, 2020 at 8:32 AM Marc Fehling  wrote:

> Pushkar,
>
> would you check the `detailed.log` file in the build folder in which you
> configured deal.II with cmake and find the configuration details for PETSc.
>
> Does the PETSc folder specified in the log file contain the requested
> header files? The header files should be located in an include folder,
> i.e., /path/to/petsc/include
>
> Best,
> Marc
>
> On Thursday, November 26, 2020 at 7:47:50 PM UTC-7 pushkar...@gmail.com
> wrote:
>
>> Yes I did follow the above instructions but I am still facing the same
>> issue .
>>
>> On Fri, Nov 27, 2020 at 3:53 AM Marc Fehling  wrote:
>>
>>> Hi Pushkar!
>>>
>>> It appears the PETSc has been found during the configuration of deal.II
>>> with cmake, but you can not find the header files of the PETSc libraries
>>> during compilation.
>>>
>>> Did you follow all instructions on how to interface deal.II to PETSc on
>>> this particular guide
>>> ?
>>>
>>> Marc
>>> On Thursday, November 26, 2020 at 5:24:58 AM UTC-7 pushkar...@gmail.com
>>> wrote:
>>>
 Dear deal.II community,

 I am installing deal.II 9.0.0 as I wish to run PRIMS-PF on it wherein
 during the process I ran into certain issues as :
  In file included from
 /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
  from
 /home/pushkar/dealii-9.0.0/source/dofs/dof_accessor_get.cc:21:
 /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12:
 fatal error: petscvec.h: No such file or directory
32 | #  include 
   |^~~~
 compilation terminated.
 make[2]: *** [source/dofs/CMakeFiles/obj_dofs_debug.dir/build.make:160:
 source/dofs/CMakeFiles/obj_dofs_debug.dir/dof_accessor_get.cc.o] Error 1
 make[1]: *** [CMakeFiles/Makefile2:3588:
 source/dofs/CMakeFiles/obj_dofs_debug.dir/all] Error 2
 make[1]: *** Waiting for unfinished jobs
 [ 48%] Building CXX object
 source/base/CMakeFiles/obj_base_debug.dir/multithread_info.cc.o
 In file included from
 /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
  from
 /home/pushkar/dealii-9.0.0/source/algorithms/operator.cc:30:
 /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12:
 fatal error: petscvec.h: No such file or directory
32 | #  include 
   |^~~~
 compilation terminated.
 make[2]: ***
 [source/algorithms/CMakeFiles/obj_algorithms_debug.dir/build.make:82:
 source/algorithms/CMakeFiles/obj_algorithms_debug.dir/operator.cc.o] Error 
 1
 make[1]: *** [CMakeFiles/Makefile2:4209:
 source/algorithms/CMakeFiles/obj_algorithms_debug.dir/all] Error 2
 [ 48%] Building CXX object
 source/base/CMakeFiles/obj_base_debug.dir/named_selection.cc.o
 In file included from
 /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
  from
 /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_block_vector.h:24,
  from
 /home/pushkar/dealii-9.0.0/source/multigrid/mg_base.cc:21:
 /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12:
 fatal error: petscvec.h: No such file or directory
32 | #  include 
   |^~~~
 compilation terminated.
 make[2]: ***
 [source/multigrid/CMakeFiles/obj_multigrid_debug.dir/build.make:82:
 source/multigrid/CMakeFiles/obj_multigrid_debug.dir/mg_base.cc.o] Error 1
 make[1]: *** [CMakeFiles/Makefile2:4047:
 source/multigrid/CMakeFiles/obj_multigrid_debug.dir/all] Error 2
 [ 48%] Building CXX object
 source/distributed/CMakeFiles/obj_distributed_debug.dir/solution_transfer.cc.o
 /home/pushkar/dealii-9.0.0/source/base/mpi.cc:38:12: fatal error:
 petscsys.h: No such file or directory
38 | #  include 
   |^~~~
 compilation terminated.
 make[2]: *** [source/base/CMakeFiles/obj_base_debug.dir/build.make:368:
 source/base/CMakeFiles/obj_base_debug.dir/mpi.cc.o] Error 1
 make[2]: *** Waiting for unfinished jobs
 [ 48%] Building CXX object
 source/distributed/CMakeFiles/obj_distributed_debug.dir/tria.cc.o
 In file included from
 /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
  from
 /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_block_vector.h:24,
  fro

Re: [deal.II] Re: DEAL.II INSTALLATION ERROR

[Marc Fehling]

Pushkar,

would you check the `detailed.log` file in the build folder in which you 
configured deal.II with cmake and find the configuration details for PETSc.

Does the PETSc folder specified in the log file contain the requested 
header files? The header files should be located in an include folder, 
i.e., /path/to/petsc/include

Best,
Marc

On Thursday, November 26, 2020 at 7:47:50 PM UTC-7 pushkar...@gmail.com 
wrote:

> Yes I did follow the above instructions but I am still facing the same 
> issue . 
>
> On Fri, Nov 27, 2020 at 3:53 AM Marc Fehling  wrote:
>
>> Hi Pushkar!
>>
>> It appears the PETSc has been found during the configuration of deal.II 
>> with cmake, but you can not find the header files of the PETSc libraries 
>> during compilation.
>>
>> Did you follow all instructions on how to interface deal.II to PETSc on 
>> this particular guide 
>> ?
>>
>> Marc
>> On Thursday, November 26, 2020 at 5:24:58 AM UTC-7 pushkar...@gmail.com 
>> wrote:
>>
>>> Dear deal.II community,
>>>
>>> I am installing deal.II 9.0.0 as I wish to run PRIMS-PF on it wherein 
>>> during the process I ran into certain issues as :
>>>  In file included from 
>>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
>>>  from 
>>> /home/pushkar/dealii-9.0.0/source/dofs/dof_accessor_get.cc:21:
>>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12: 
>>> fatal error: petscvec.h: No such file or directory
>>>32 | #  include 
>>>   |^~~~
>>> compilation terminated.
>>> make[2]: *** [source/dofs/CMakeFiles/obj_dofs_debug.dir/build.make:160: 
>>> source/dofs/CMakeFiles/obj_dofs_debug.dir/dof_accessor_get.cc.o] Error 1
>>> make[1]: *** [CMakeFiles/Makefile2:3588: 
>>> source/dofs/CMakeFiles/obj_dofs_debug.dir/all] Error 2
>>> make[1]: *** Waiting for unfinished jobs
>>> [ 48%] Building CXX object 
>>> source/base/CMakeFiles/obj_base_debug.dir/multithread_info.cc.o
>>> In file included from 
>>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
>>>  from 
>>> /home/pushkar/dealii-9.0.0/source/algorithms/operator.cc:30:
>>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12: 
>>> fatal error: petscvec.h: No such file or directory
>>>32 | #  include 
>>>   |^~~~
>>> compilation terminated.
>>> make[2]: *** 
>>> [source/algorithms/CMakeFiles/obj_algorithms_debug.dir/build.make:82: 
>>> source/algorithms/CMakeFiles/obj_algorithms_debug.dir/operator.cc.o] Error 1
>>> make[1]: *** [CMakeFiles/Makefile2:4209: 
>>> source/algorithms/CMakeFiles/obj_algorithms_debug.dir/all] Error 2
>>> [ 48%] Building CXX object 
>>> source/base/CMakeFiles/obj_base_debug.dir/named_selection.cc.o
>>> In file included from 
>>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
>>>  from 
>>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_block_vector.h:24,
>>>  from 
>>> /home/pushkar/dealii-9.0.0/source/multigrid/mg_base.cc:21:
>>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12: 
>>> fatal error: petscvec.h: No such file or directory
>>>32 | #  include 
>>>   |^~~~
>>> compilation terminated.
>>> make[2]: *** 
>>> [source/multigrid/CMakeFiles/obj_multigrid_debug.dir/build.make:82: 
>>> source/multigrid/CMakeFiles/obj_multigrid_debug.dir/mg_base.cc.o] Error 1
>>> make[1]: *** [CMakeFiles/Makefile2:4047: 
>>> source/multigrid/CMakeFiles/obj_multigrid_debug.dir/all] Error 2
>>> [ 48%] Building CXX object 
>>> source/distributed/CMakeFiles/obj_distributed_debug.dir/solution_transfer.cc.o
>>> /home/pushkar/dealii-9.0.0/source/base/mpi.cc:38:12: fatal error: 
>>> petscsys.h: No such file or directory
>>>38 | #  include 
>>>   |^~~~
>>> compilation terminated.
>>> make[2]: *** [source/base/CMakeFiles/obj_base_debug.dir/build.make:368: 
>>> source/base/CMakeFiles/obj_base_debug.dir/mpi.cc.o] Error 1
>>> make[2]: *** Waiting for unfinished jobs
>>> [ 48%] Building CXX object 
>>> source/distributed/CMakeFiles/obj_distributed_debug.dir/tria.cc.o
>>> In file included from 
>>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
>>>  from 
>>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_block_vector.h:24,
>>>  from 
>>> /home/pushkar/dealii-9.0.0/source/lac/block_matrix_array.cc:23:
>>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12: 
>>> fatal error: petscvec.h: No such file or directory
>>>32 | #  include 
>>>   |^~~~
>>> compilation terminated.
>>> make[2]: *** [source/lac/CMakeFiles/obj_lac_debug.dir/build.make:82: 
>>> source/lac/CMakeFiles/obj_lac_debug.dir/block_matrix_array.cc.o] Error 1
>>> make[1]: *** [CMakeFiles/Makefile2:3615: 
>>> source/

Re: [deal.II] Re: DEAL.II INSTALLATION ERROR

[Pushkar Pandit]

Yes I did follow the above instructions but I am still facing the same
issue .

On Fri, Nov 27, 2020 at 3:53 AM Marc Fehling  wrote:

> Hi Pushkar!
>
> It appears the PETSc has been found during the configuration of deal.II
> with cmake, but you can not find the header files of the PETSc libraries
> during compilation.
>
> Did you follow all instructions on how to interface deal.II to PETSc on
> this particular guide
> ?
>
> Marc
> On Thursday, November 26, 2020 at 5:24:58 AM UTC-7 pushkar...@gmail.com
> wrote:
>
>> Dear deal.II community,
>>
>> I am installing deal.II 9.0.0 as I wish to run PRIMS-PF on it wherein
>> during the process I ran into certain issues as :
>>  In file included from
>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
>>  from
>> /home/pushkar/dealii-9.0.0/source/dofs/dof_accessor_get.cc:21:
>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12:
>> fatal error: petscvec.h: No such file or directory
>>32 | #  include 
>>   |^~~~
>> compilation terminated.
>> make[2]: *** [source/dofs/CMakeFiles/obj_dofs_debug.dir/build.make:160:
>> source/dofs/CMakeFiles/obj_dofs_debug.dir/dof_accessor_get.cc.o] Error 1
>> make[1]: *** [CMakeFiles/Makefile2:3588:
>> source/dofs/CMakeFiles/obj_dofs_debug.dir/all] Error 2
>> make[1]: *** Waiting for unfinished jobs
>> [ 48%] Building CXX object
>> source/base/CMakeFiles/obj_base_debug.dir/multithread_info.cc.o
>> In file included from
>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
>>  from
>> /home/pushkar/dealii-9.0.0/source/algorithms/operator.cc:30:
>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12:
>> fatal error: petscvec.h: No such file or directory
>>32 | #  include 
>>   |^~~~
>> compilation terminated.
>> make[2]: ***
>> [source/algorithms/CMakeFiles/obj_algorithms_debug.dir/build.make:82:
>> source/algorithms/CMakeFiles/obj_algorithms_debug.dir/operator.cc.o] Error 1
>> make[1]: *** [CMakeFiles/Makefile2:4209:
>> source/algorithms/CMakeFiles/obj_algorithms_debug.dir/all] Error 2
>> [ 48%] Building CXX object
>> source/base/CMakeFiles/obj_base_debug.dir/named_selection.cc.o
>> In file included from
>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
>>  from
>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_block_vector.h:24,
>>  from
>> /home/pushkar/dealii-9.0.0/source/multigrid/mg_base.cc:21:
>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12:
>> fatal error: petscvec.h: No such file or directory
>>32 | #  include 
>>   |^~~~
>> compilation terminated.
>> make[2]: ***
>> [source/multigrid/CMakeFiles/obj_multigrid_debug.dir/build.make:82:
>> source/multigrid/CMakeFiles/obj_multigrid_debug.dir/mg_base.cc.o] Error 1
>> make[1]: *** [CMakeFiles/Makefile2:4047:
>> source/multigrid/CMakeFiles/obj_multigrid_debug.dir/all] Error 2
>> [ 48%] Building CXX object
>> source/distributed/CMakeFiles/obj_distributed_debug.dir/solution_transfer.cc.o
>> /home/pushkar/dealii-9.0.0/source/base/mpi.cc:38:12: fatal error:
>> petscsys.h: No such file or directory
>>38 | #  include 
>>   |^~~~
>> compilation terminated.
>> make[2]: *** [source/base/CMakeFiles/obj_base_debug.dir/build.make:368:
>> source/base/CMakeFiles/obj_base_debug.dir/mpi.cc.o] Error 1
>> make[2]: *** Waiting for unfinished jobs
>> [ 48%] Building CXX object
>> source/distributed/CMakeFiles/obj_distributed_debug.dir/tria.cc.o
>> In file included from
>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
>>  from
>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_block_vector.h:24,
>>  from
>> /home/pushkar/dealii-9.0.0/source/lac/block_matrix_array.cc:23:
>> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12:
>> fatal error: petscvec.h: No such file or directory
>>32 | #  include 
>>   |^~~~
>> compilation terminated.
>> make[2]: *** [source/lac/CMakeFiles/obj_lac_debug.dir/build.make:82:
>> source/lac/CMakeFiles/obj_lac_debug.dir/block_matrix_array.cc.o] Error 1
>> make[1]: *** [CMakeFiles/Makefile2:3615:
>> source/lac/CMakeFiles/obj_lac_debug.dir/all] Error 2
>> [ 48%] Building CXX object
>> source/distributed/CMakeFiles/obj_distributed_debug.dir/tria_base.cc.o
>> In file included from
>> /home/pushkar/dealii-9.0.0/include/deal.II/hp/fe_values.h:24,
>>  from
>> /home/pushkar/dealii-9.0.0/include/deal.II/numerics/data_out_dof_data.h:30,
>>  from
>> /home/pushkar/dealii-9.0.0/include/deal.II/numerics/data_out.h:22,
>>  from
>> /home/pushkar/dealii-9.0.0/source/numerics/data_out.cc:17:
>> /home/pushkar/dealii-9.0.0/include/deal

[deal.II] Re: DEAL.II INSTALLATION ERROR

[Marc Fehling]

Hi Pushkar!

It appears the PETSc has been found during the configuration of deal.II 
with cmake, but you can not find the header files of the PETSc libraries 
during compilation.

Did you follow all instructions on how to interface deal.II to PETSc on 
this particular guide 
?

Marc
On Thursday, November 26, 2020 at 5:24:58 AM UTC-7 pushkar...@gmail.com 
wrote:

> Dear deal.II community,
>
> I am installing deal.II 9.0.0 as I wish to run PRIMS-PF on it wherein 
> during the process I ran into certain issues as :
>  In file included from 
> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
>  from 
> /home/pushkar/dealii-9.0.0/source/dofs/dof_accessor_get.cc:21:
> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12: 
> fatal error: petscvec.h: No such file or directory
>32 | #  include 
>   |^~~~
> compilation terminated.
> make[2]: *** [source/dofs/CMakeFiles/obj_dofs_debug.dir/build.make:160: 
> source/dofs/CMakeFiles/obj_dofs_debug.dir/dof_accessor_get.cc.o] Error 1
> make[1]: *** [CMakeFiles/Makefile2:3588: 
> source/dofs/CMakeFiles/obj_dofs_debug.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs
> [ 48%] Building CXX object 
> source/base/CMakeFiles/obj_base_debug.dir/multithread_info.cc.o
> In file included from 
> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
>  from 
> /home/pushkar/dealii-9.0.0/source/algorithms/operator.cc:30:
> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12: 
> fatal error: petscvec.h: No such file or directory
>32 | #  include 
>   |^~~~
> compilation terminated.
> make[2]: *** 
> [source/algorithms/CMakeFiles/obj_algorithms_debug.dir/build.make:82: 
> source/algorithms/CMakeFiles/obj_algorithms_debug.dir/operator.cc.o] Error 1
> make[1]: *** [CMakeFiles/Makefile2:4209: 
> source/algorithms/CMakeFiles/obj_algorithms_debug.dir/all] Error 2
> [ 48%] Building CXX object 
> source/base/CMakeFiles/obj_base_debug.dir/named_selection.cc.o
> In file included from 
> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
>  from 
> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_block_vector.h:24,
>  from 
> /home/pushkar/dealii-9.0.0/source/multigrid/mg_base.cc:21:
> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12: 
> fatal error: petscvec.h: No such file or directory
>32 | #  include 
>   |^~~~
> compilation terminated.
> make[2]: *** 
> [source/multigrid/CMakeFiles/obj_multigrid_debug.dir/build.make:82: 
> source/multigrid/CMakeFiles/obj_multigrid_debug.dir/mg_base.cc.o] Error 1
> make[1]: *** [CMakeFiles/Makefile2:4047: 
> source/multigrid/CMakeFiles/obj_multigrid_debug.dir/all] Error 2
> [ 48%] Building CXX object 
> source/distributed/CMakeFiles/obj_distributed_debug.dir/solution_transfer.cc.o
> /home/pushkar/dealii-9.0.0/source/base/mpi.cc:38:12: fatal error: 
> petscsys.h: No such file or directory
>38 | #  include 
>   |^~~~
> compilation terminated.
> make[2]: *** [source/base/CMakeFiles/obj_base_debug.dir/build.make:368: 
> source/base/CMakeFiles/obj_base_debug.dir/mpi.cc.o] Error 1
> make[2]: *** Waiting for unfinished jobs
> [ 48%] Building CXX object 
> source/distributed/CMakeFiles/obj_distributed_debug.dir/tria.cc.o
> In file included from 
> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
>  from 
> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_block_vector.h:24,
>  from 
> /home/pushkar/dealii-9.0.0/source/lac/block_matrix_array.cc:23:
> /home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12: 
> fatal error: petscvec.h: No such file or directory
>32 | #  include 
>   |^~~~
> compilation terminated.
> make[2]: *** [source/lac/CMakeFiles/obj_lac_debug.dir/build.make:82: 
> source/lac/CMakeFiles/obj_lac_debug.dir/block_matrix_array.cc.o] Error 1
> make[1]: *** [CMakeFiles/Makefile2:3615: 
> source/lac/CMakeFiles/obj_lac_debug.dir/all] Error 2
> [ 48%] Building CXX object 
> source/distributed/CMakeFiles/obj_distributed_debug.dir/tria_base.cc.o
> In file included from 
> /home/pushkar/dealii-9.0.0/include/deal.II/hp/fe_values.h:24,
>  from 
> /home/pushkar/dealii-9.0.0/include/deal.II/numerics/data_out_dof_data.h:30,
>  from 
> /home/pushkar/dealii-9.0.0/include/deal.II/numerics/data_out.h:22,
>  from 
> /home/pushkar/dealii-9.0.0/source/numerics/data_out.cc:17:
> /home/pushkar/dealii-9.0.0/include/deal.II/fe/fe_values.h:48:12: fatal 
> error: petsc.h: No such file or directory
>48 | #  include 
>   |^
> compilation terminated.
> make[2]: *** 
> [source/numerics/CMakeFiles/obj_n

[deal.II] DEAL.II INSTALLATION ERROR

[pushkar...@gmail.com]

Dear deal.II community,

I am installing deal.II 9.0.0 as I wish to run PRIMS-PF on it wherein 
during the process I ran into certain issues as :
 In file included from 
/home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
 from 
/home/pushkar/dealii-9.0.0/source/dofs/dof_accessor_get.cc:21:
/home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12: 
fatal error: petscvec.h: No such file or directory
   32 | #  include 
  |^~~~
compilation terminated.
make[2]: *** [source/dofs/CMakeFiles/obj_dofs_debug.dir/build.make:160: 
source/dofs/CMakeFiles/obj_dofs_debug.dir/dof_accessor_get.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:3588: 
source/dofs/CMakeFiles/obj_dofs_debug.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs
[ 48%] Building CXX object 
source/base/CMakeFiles/obj_base_debug.dir/multithread_info.cc.o
In file included from 
/home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
 from 
/home/pushkar/dealii-9.0.0/source/algorithms/operator.cc:30:
/home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12: 
fatal error: petscvec.h: No such file or directory
   32 | #  include 
  |^~~~
compilation terminated.
make[2]: *** 
[source/algorithms/CMakeFiles/obj_algorithms_debug.dir/build.make:82: 
source/algorithms/CMakeFiles/obj_algorithms_debug.dir/operator.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:4209: 
source/algorithms/CMakeFiles/obj_algorithms_debug.dir/all] Error 2
[ 48%] Building CXX object 
source/base/CMakeFiles/obj_base_debug.dir/named_selection.cc.o
In file included from 
/home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
 from 
/home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_block_vector.h:24,
 from 
/home/pushkar/dealii-9.0.0/source/multigrid/mg_base.cc:21:
/home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12: 
fatal error: petscvec.h: No such file or directory
   32 | #  include 
  |^~~~
compilation terminated.
make[2]: *** 
[source/multigrid/CMakeFiles/obj_multigrid_debug.dir/build.make:82: 
source/multigrid/CMakeFiles/obj_multigrid_debug.dir/mg_base.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:4047: 
source/multigrid/CMakeFiles/obj_multigrid_debug.dir/all] Error 2
[ 48%] Building CXX object 
source/distributed/CMakeFiles/obj_distributed_debug.dir/solution_transfer.cc.o
/home/pushkar/dealii-9.0.0/source/base/mpi.cc:38:12: fatal error: 
petscsys.h: No such file or directory
   38 | #  include 
  |^~~~
compilation terminated.
make[2]: *** [source/base/CMakeFiles/obj_base_debug.dir/build.make:368: 
source/base/CMakeFiles/obj_base_debug.dir/mpi.cc.o] Error 1
make[2]: *** Waiting for unfinished jobs
[ 48%] Building CXX object 
source/distributed/CMakeFiles/obj_distributed_debug.dir/tria.cc.o
In file included from 
/home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
 from 
/home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_block_vector.h:24,
 from 
/home/pushkar/dealii-9.0.0/source/lac/block_matrix_array.cc:23:
/home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12: 
fatal error: petscvec.h: No such file or directory
   32 | #  include 
  |^~~~
compilation terminated.
make[2]: *** [source/lac/CMakeFiles/obj_lac_debug.dir/build.make:82: 
source/lac/CMakeFiles/obj_lac_debug.dir/block_matrix_array.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:3615: 
source/lac/CMakeFiles/obj_lac_debug.dir/all] Error 2
[ 48%] Building CXX object 
source/distributed/CMakeFiles/obj_distributed_debug.dir/tria_base.cc.o
In file included from 
/home/pushkar/dealii-9.0.0/include/deal.II/hp/fe_values.h:24,
 from 
/home/pushkar/dealii-9.0.0/include/deal.II/numerics/data_out_dof_data.h:30,
 from 
/home/pushkar/dealii-9.0.0/include/deal.II/numerics/data_out.h:22,
 from 
/home/pushkar/dealii-9.0.0/source/numerics/data_out.cc:17:
/home/pushkar/dealii-9.0.0/include/deal.II/fe/fe_values.h:48:12: fatal 
error: petsc.h: No such file or directory
   48 | #  include 
  |^
compilation terminated.
make[2]: *** 
[source/numerics/CMakeFiles/obj_numerics_debug.dir/build.make:82: 
source/numerics/CMakeFiles/obj_numerics_debug.dir/data_out.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:3399: 
source/numerics/CMakeFiles/obj_numerics_debug.dir/all] Error 2
[ 48%] Building CXX object 
source/distributed/CMakeFiles/obj_distributed_debug.dir/shared_tria.cc.o
In file included from 
/home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_parallel_vector.h:28,
 from 
/home/pushkar/dealii-9.0.0/source/distributed/solution_transfer.cc:25:
/home/pushkar/dealii-9.0.0/include/deal.II/lac/petsc_vector_base.h:32:12: 
fatal error: petscvec.h: No such

Re: [deal.II] Installation error on Haswell nodes on Cori at NERSC (failed AVX512 support)

[Stephen DeWitt]

Dear Martin,
Thank you for your response. I deleted everything in my build directory and 
then it worked. I thought that deleting the CMakeCache.txt file and 
CMakeFiles would be enough (in other cases it has been), but evidently it 
wasn't enough here.

Thanks again,
Steve

On Wednesday, July 10, 2019 at 10:04:32 AM UTC-4, Martin Kronbichler wrote:
>
> Dear Steve,
>
> From what I can see the failure is for the expand_instantiations script of 
> deal.II, which is compiled as part of deal.II. It uses slightly different 
> flags as the full install, but assuming that you either passed -xHASWELL or 
> -xCORE-AVX2 to CMAKE_CXX_FLAGS it should not generate that code. Before we 
> look into the flags used for compilation, a basic question: Did you start 
> with a clean build directory without any file left over from a more 
> advanced architecture with AVX512 support?
>
> Best,
> Martin
> On 10.07.19 15:56, Stephen DeWitt wrote:
>
> Hello, 
> I'm trying to install deal.II on the Haswell nodes on Cori at NERSC using 
> the Intel compiler. I'm using deal.II version 9.0, because support for a 
> few of the function calls I make were dropped in v9.1 and I haven't had a 
> chance to modify the sections of the code. In my CMake command, I'm adding 
> either the -xHASWELL or -xCORE-AVX2 flags to get the right level of 
> vectorization for this architecture (AVX). The CMake output is what I 
> expect:
>
> -- Performing Test DEAL_II_HAVE_SSE2
> -- Performing Test DEAL_II_HAVE_SSE2 - Success
> -- Performing Test DEAL_II_HAVE_AVX
> -- Performing Test DEAL_II_HAVE_AVX - Success
> -- Performing Test DEAL_II_HAVE_AVX512
> -- Performing Test DEAL_II_HAVE_AVX512 - Failed
> -- Performing Test DEAL_II_HAVE_OPENMP_SIMD
> -- Performing Test DEAL_II_HAVE_OPENMP_SIMD - Success
>
> However, when I try to compile I get this error:
>
> [ 32%] Built target obj_umfpack_DL_STORE_release
> [ 34%] Built target obj_amd_global_release
> [ 35%] Built target obj_amd_long_release
> [ 36%] Built target obj_amd_int_release
> [ 37%] Built target obj_muparser_release
> [ 37%] Built target obj_sundials_inst
> Scanning dependencies of target obj_sundials_release
> [ 37%] Building CXX object 
> source/sundials/CMakeFiles/obj_sundials_release.dir/arkode.cc.o
> [ 37%] Building CXX object 
> source/sundials/CMakeFiles/obj_sundials_release.dir/ida.cc.o
> [ 37%] Building CXX object 
> source/sundials/CMakeFiles/obj_sundials_release.dir/copy.cc.o
> [ 38%] Building CXX object 
> source/sundials/CMakeFiles/obj_sundials_release.dir/kinsol.cc.o
> [ 38%] Built target obj_sundials_release
> [ 38%] Generating data_out_dof_data.inst
>
> Please verify that both the operating system and the processor support 
> Intel(R) AVX512F, ADX, AVX512ER, AVX512PF and AVX512CD instructions.
>
> source/numerics/CMakeFiles/obj_numerics_inst.dir/build.make:91: recipe for 
> target 'source/numerics/data_out_dof_data.inst' failed
> make[2]: *** [source/numerics/data_out_dof_data.inst] Error 1
> CMakeFiles/Makefile2:1860: recipe for target 
> 'source/numerics/CMakeFiles/obj_numerics_inst.dir/all' failed
> make[1]: *** [source/numerics/CMakeFiles/obj_numerics_inst.dir/all] Error 2
> Makefile:129: recipe for target 'all' failed
> make: *** [all] Error 2
>
> It seems to me that it is looking for AVX512 support and generating an 
> error when it doesn't find it. But why would it look for AVX512 support if 
> DEAL_II_HAVE_AVX512 failed? I haven't had this issue when installing on 
> other machines that support AVX but not AVX512.
>
> Thanks for any insight you have,
> Steve
> -- 
> 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
> --- 
> You received this message because you are subscribed to the Google Groups 
> "deal.II User Group" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to dea...@googlegroups.com .
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/dealii/b36fd46d-2dff-41f4-8762-8ffad6ad4da1%40googlegroups.com
>  
> 
> .
> For more options, visit https://groups.google.com/d/optout.
>
>

-- 
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
--- 
You received this message because you are subscribed to the Google Groups 
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to dealii+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/4064831c-921d-4cd0-9fde-a726db3619d2%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

Re: [deal.II] Installation error on Haswell nodes on Cori at NERSC (failed AVX512 support)

[Martin Kronbichler]

Dear Steve,

>From what I can see the failure is for the expand_instantiations script
of deal.II, which is compiled as part of deal.II. It uses slightly
different flags as the full install, but assuming that you either passed
-xHASWELL or -xCORE-AVX2 to CMAKE_CXX_FLAGS it should not generate that
code. Before we look into the flags used for compilation, a basic
question: Did you start with a clean build directory without any file
left over from a more advanced architecture with AVX512 support?

Best,
Martin

On 10.07.19 15:56, Stephen DeWitt wrote:
> Hello,
> I'm trying to install deal.II on the Haswell nodes on Cori at NERSC
> using the Intel compiler. I'm using deal.II version 9.0, because
> support for a few of the function calls I make were dropped in v9.1
> and I haven't had a chance to modify the sections of the code. In my
> CMake command, I'm adding either the -xHASWELL or -xCORE-AVX2 flags to
> get the right level of vectorization for this architecture (AVX). The
> CMake output is what I expect:
>
> |
> -- Performing Test DEAL_II_HAVE_SSE2
> -- Performing Test DEAL_II_HAVE_SSE2 - Success
> -- Performing Test DEAL_II_HAVE_AVX
> -- Performing Test DEAL_II_HAVE_AVX - Success
> -- Performing Test DEAL_II_HAVE_AVX512
> -- Performing Test DEAL_II_HAVE_AVX512 - Failed
> -- Performing Test DEAL_II_HAVE_OPENMP_SIMD
> -- Performing Test DEAL_II_HAVE_OPENMP_SIMD - Success
> |
>
> However, when I try to compile I get this error:
>
> |
> [ 32%] Built target obj_umfpack_DL_STORE_release
> [ 34%] Built target obj_amd_global_release
> [ 35%] Built target obj_amd_long_release
> [ 36%] Built target obj_amd_int_release
> [ 37%] Built target obj_muparser_release
> [ 37%] Built target obj_sundials_inst
> Scanning dependencies of target obj_sundials_release
> [ 37%] Building CXX object
> source/sundials/CMakeFiles/obj_sundials_release.dir/arkode.cc.o
> [ 37%] Building CXX object
> source/sundials/CMakeFiles/obj_sundials_release.dir/ida.cc.o
> [ 37%] Building CXX object
> source/sundials/CMakeFiles/obj_sundials_release.dir/copy.cc.o
> [ 38%] Building CXX object
> source/sundials/CMakeFiles/obj_sundials_release.dir/kinsol.cc.o
> [ 38%] Built target obj_sundials_release
> [ 38%] Generating data_out_dof_data.inst
>
> Please verify that both the operating system and the processor support
> Intel(R) AVX512F, ADX, AVX512ER, AVX512PF and AVX512CD instructions.
>
> source/numerics/CMakeFiles/obj_numerics_inst.dir/build.make:91: recipe
> for target 'source/numerics/data_out_dof_data.inst' failed
> make[2]: *** [source/numerics/data_out_dof_data.inst] Error 1
> CMakeFiles/Makefile2:1860: recipe for target
> 'source/numerics/CMakeFiles/obj_numerics_inst.dir/all' failed
> make[1]: *** [source/numerics/CMakeFiles/obj_numerics_inst.dir/all]
> Error 2
> Makefile:129: recipe for target 'all' failed
> make: *** [all] Error 2
> |
>
> It seems to me that it is looking for AVX512 support and generating an
> error when it doesn't find it. But why would it look for AVX512
> support if DEAL_II_HAVE_AVX512 failed? I haven't had this issue when
> installing on other machines that support AVX but not AVX512.
>
> Thanks for any insight you have,
> Steve
> -- 
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[deal.II] Installation error on Haswell nodes on Cori at NERSC (failed AVX512 support)

[Stephen DeWitt]

Hello,
I'm trying to install deal.II on the Haswell nodes on Cori at NERSC using 
the Intel compiler. I'm using deal.II version 9.0, because support for a 
few of the function calls I make were dropped in v9.1 and I haven't had a 
chance to modify the sections of the code. In my CMake command, I'm adding 
either the -xHASWELL or -xCORE-AVX2 flags to get the right level of 
vectorization for this architecture (AVX). The CMake output is what I 
expect:

-- Performing Test DEAL_II_HAVE_SSE2
-- Performing Test DEAL_II_HAVE_SSE2 - Success
-- Performing Test DEAL_II_HAVE_AVX
-- Performing Test DEAL_II_HAVE_AVX - Success
-- Performing Test DEAL_II_HAVE_AVX512
-- Performing Test DEAL_II_HAVE_AVX512 - Failed
-- Performing Test DEAL_II_HAVE_OPENMP_SIMD
-- Performing Test DEAL_II_HAVE_OPENMP_SIMD - Success

However, when I try to compile I get this error:

[ 32%] Built target obj_umfpack_DL_STORE_release
[ 34%] Built target obj_amd_global_release
[ 35%] Built target obj_amd_long_release
[ 36%] Built target obj_amd_int_release
[ 37%] Built target obj_muparser_release
[ 37%] Built target obj_sundials_inst
Scanning dependencies of target obj_sundials_release
[ 37%] Building CXX object 
source/sundials/CMakeFiles/obj_sundials_release.dir/arkode.cc.o
[ 37%] Building CXX object 
source/sundials/CMakeFiles/obj_sundials_release.dir/ida.cc.o
[ 37%] Building CXX object 
source/sundials/CMakeFiles/obj_sundials_release.dir/copy.cc.o
[ 38%] Building CXX object 
source/sundials/CMakeFiles/obj_sundials_release.dir/kinsol.cc.o
[ 38%] Built target obj_sundials_release
[ 38%] Generating data_out_dof_data.inst

Please verify that both the operating system and the processor support 
Intel(R) AVX512F, ADX, AVX512ER, AVX512PF and AVX512CD instructions.

source/numerics/CMakeFiles/obj_numerics_inst.dir/build.make:91: recipe for 
target 'source/numerics/data_out_dof_data.inst' failed
make[2]: *** [source/numerics/data_out_dof_data.inst] Error 1
CMakeFiles/Makefile2:1860: recipe for target 
'source/numerics/CMakeFiles/obj_numerics_inst.dir/all' failed
make[1]: *** [source/numerics/CMakeFiles/obj_numerics_inst.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

It seems to me that it is looking for AVX512 support and generating an 
error when it doesn't find it. But why would it look for AVX512 support if 
DEAL_II_HAVE_AVX512 failed? I haven't had this issue when installing on 
other machines that support AVX but not AVX512.

Thanks for any insight you have,
Steve

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Re: [deal.II] Installation error

['Uwe Köcher' via deal . II User Group]

alternatively,
you could run the same configuration on a workstation and copy the tmp/src
and tmp/unpack to your cluster.

Maybe you need the developer_mode as given by the last line of the
config file as well - I'm not sure on that since I never run it without
git access.

Best
  Uwe

On Friday, 22 February 2019 17:00:39 UTC-6, Wolfgang Bangerth wrote:
>
> On 2/22/19 4:20 AM, 刘泽 wrote: 
> > fatal: unable to access 'https://github.com/dealii/dealii.git/': Unable 
> > to communicate securely with peer: requested domain name does not match 
> > the server's certificate. 
>
> I suspect you are calling candi from a node on the cluster that does not 
> have access to the internet via http. This is a common configuration for 
> clusters. 
>
> Talk to your system administrator. There is typically a way to set a 
> proxy somewhere (after which you need to tell git about it) so that git 
> can access http sites from the cluster as well. 
>
> Best 
>   W. 
>
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>

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Re: [deal.II] Installation error

[Wolfgang Bangerth]

On 2/22/19 4:20 AM, 刘泽 wrote:
> fatal: unable to access 'https://github.com/dealii/dealii.git/': Unable 
> to communicate securely with peer: requested domain name does not match 
> the server's certificate.

I suspect you are calling candi from a node on the cluster that does not 
have access to the internet via http. This is a common configuration for 
clusters.

Talk to your system administrator. There is typically a way to set a 
proxy somewhere (after which you need to tell git about it) so that git 
can access http sites from the cluster as well.

Best
  W.


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

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[deal.II] Installation error

[刘泽]

Dear all,

 

I was trying to install dealii version 9.0.1 on department cluster using 
candi, 

 

Before installing it, I install openmpi-3.0.0-intel

 

git clone https://github.com/dealii/candi

cd candi

./candi.sh -j 12  
--platform=./deal.II-toolchain/platforms/supported/linux_cluster.platform 
-p /opt/bin/

 

but I got the following messages:

 

Number of (at most) build processes to use: PROCS=12

 

---

Packages:

load:dealii-prepare

once:git

once:opencascade

once:parmetis

once:hdf5

once:p4est

once:trilinos

once:petsc

once:slepc

dealii

 

---

Building stable releases of deal.II-toolchain packages.

 

---

Currently loaded modulefiles:

No Modulefiles Currently Loaded.

 

 

Compiler Variables:

---

CC variable not set, but default mpicc found.

CC  = /opt/openmpi-3.0.0-intel/bin/mpicc

CXX variable not set, but default mpicxx found.

CXX = /opt/openmpi-3.0.0-intel/bin/mpicxx

FC variable not set, but default mpif90 found.

FC  = /opt/openmpi-3.0.0-intel/bin/mpif90

FF variable not set, but default mpif77 found.

FF  = /opt/openmpi-3.0.0-intel/bin/mpif77

 

 

After that I got the following error:

 

candi tries now to download, configure, build and install:

 

Project:  deal.II-toolchain

Platform: ./deal.II-toolchain/platforms/supported/linux_cluster.platform

 

Loading dealii-prepare

Skipping git

Skipping opencascade

Skipping parmetis

Skipping hdf5

Skipping p4est

trilinos: configuration with ParMETIS

Skipping trilinos

PETSc: configuration with ParMETIS

Skipping petsc

Skipping slepc

deal.II: configuration with METIS

deal.II: configuration with P4EST

deal.II: configuration with HDF5

deal.II: configuration with TRILINOS

deal.II: configuration with PETSC

deal.II: configuration with SLEPC

deal.II: configuration with OPENCASCADE

Fetching dealii v9.0.1

Previous HEAD position was 097bf59... update VERSION for release

Switched to branch 'master'

Your branch is up-to-date with 'origin/master'.

fatal: unable to access 'https://github.com/dealii/dealii.git/': Unable to 
communicate securely with peer: requested domain name does not match the 
server's certificate.

Failure with exit status: 1

Exit message: candi: git pull failed

 

Many thanks for any suggestion.

 

Ze

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[deal.II] Installation error

[rp361]

After Installing dealii, 

while running step-1 of the examples using  -  make run  command, I get the 
following error,












*[ 66%] Built target step-1[100%] Run step-1 with Debug 
configuration./step-1: symbol lookup error: 
/home/student/anaconda3/lib/libmkl_intel_lp64.so: undefined symbol: 
mkl_lapack_dgetrfnpiCMakeFiles/run.dir/build.make:57: recipe for target 
'CMakeFiles/run' failedmake[3]: *** [CMakeFiles/run] Error 
127CMakeFiles/Makefile2:264: recipe for target 'CMakeFiles/run.dir/all' 
failedmake[2]: *** [CMakeFiles/run.dir/all] Error 
2CMakeFiles/Makefile2:271: recipe for target 'CMakeFiles/run.dir/rule' 
failedmake[1]: *** [CMakeFiles/run.dir/rule] Error 2Makefile:196: recipe 
for target 'run' failedmake: *** [run] Error 2*
  

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Re: [deal.II] Installation error using Ubuntu 17.10 package (missing libsmumps.so)

[Stephen DeWitt]

Hi Matthias,
Thanks! I'll pass along the advice to fetch and build the development 
version and otherwise wait for the 18.04 release.

Best,
Steve

On Thursday, April 12, 2018 at 4:36:53 PM UTC-4, Matthias Maier wrote:
>
> Status update: 
>
>  - We missed the opportunity to do a rebuild for 17.10 [1] 
>  - In the upcoming 18.04 release everything should be fine again 
>(release should be at the end of this month). 
>
> Best, 
> Matthias 
>
> [1] https://bugs.launchpad.net/ubuntu/+source/deal.ii/+bug/1729454 
>

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Re: [deal.II] Installation error using Ubuntu 17.10 package (missing libsmumps.so)

[Matthias Maier]

Status update:

 - We missed the opportunity to do a rebuild for 17.10 [1]
 - In the upcoming 18.04 release everything should be fine again
   (release should be at the end of this month).

Best,
Matthias

[1] https://bugs.launchpad.net/ubuntu/+source/deal.ii/+bug/1729454

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Re: [deal.II] Installation error using Ubuntu 17.10 package (missing libsmumps.so)

[Matthias Maier]

On Thu, Apr 12, 2018, at 14:48 CDT, Stephen DeWitt  wrote:

> Hi Matthias,
> Ok, that makes sense. 
>
> I think I have both libdeal.ii and libdeal.ii-dev, at least that's what 
> apt-get tells me if I try to install libdeal.ii-dev seperately, although I 
> haven't figured out how to use the dev version rather than the 
> auto-detected release version.

Only the 8.4.1 release is currently packaged for Debian and Ubuntu.

Given the fact that you already installed all dependencies, you can
simply fetch and build the development version via something like:

  $ git clone https://github.com/dealii/dealii
  $ mkdir dealii/build
  $ cd dealii/build
  $ cmake -DWITH_MPI=ON ..
  $ make -j  (where  is the number of parallel builds.)


I will try to fix the binary version installed in Ubuntu.

Thanks for reporting!
Matthias

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Re: [deal.II] Installation error using Ubuntu 17.10 package (missing libsmumps.so)

[Stephen DeWitt]

Hi Matthias,
Ok, that makes sense. 

I think I have both libdeal.ii and libdeal.ii-dev, at least that's what 
apt-get tells me if I try to install libdeal.ii-dev seperately, although I 
haven't figured out how to use the dev version rather than the 
auto-detected release version.

Thanks,
Steve

On Thursday, April 12, 2018 at 3:02:51 PM UTC-4, Matthias Maier wrote:
>
> Hi there, 
>
> The problem is that deal.II's CMake system records the full link 
> interface of all shared libraries - if a library changes location the 
> package has to be rebuild (in Ubuntu). If this is indeed the case I will 
> ask for this to happen. 
>
> Did you install just the library libdeal.ii, or also the development 
> package libdeal.ii-dev? 
>
> Best, 
> Matthias 
>
>
>
> On Thu, Apr 12, 2018, at 13:19 CDT, Stephen DeWitt  > wrote: 
>
> > Hello all, 
> > A PRISMS-PF user recently posted to our forum 
> >  
> that 
> > he was having an issue with the deal.ii package he got through apt-get 
> on 
> > Ubuntu 17.10. The issue seems to be related to a missing shared object 
> file 
> > for MUMPS. I booted up a Ubuntu virtual machine on VirtualBox and saw 
> the 
> > same error. 
> > 
> > What I did: 
> > 
> >1. Installed Ubuntu 17.10 on the VM 
> >2. Updated apt 
> >3. Retrieved the deal.ii package ($ sudo apt-get install libdeal.ii) 
> >4. Found the deal.ii example directory to test the installation and 
> >copied it into my home directory 
> >5. Ran CMake for step-1 
> >6. Attempted to compile step-1 (both "make release" and "make debug" 
> had 
> >the same outcome) 
> > 
> > The result: 
> > 
> > <
> https://lh3.googleusercontent.com/-CCdJka7yFUU/Ws-hCuOODDI/BAc/kvG048lCyeYJeocApENLE-toFvoR2hkoQCLcBGAs/s1600/terminal_window.tiff>
>  
>
> > 
> > I checked the '/usr/lib/' directory and found a number of MUMPS shared 
> > objects (libesmumps-5.1.so, libesmumps.a, libesmumps.so, 
> > libptesmumps-5.1.so, libptesmumps.a, and libptesmumps.so), but not 
> > "libsmumps.so". I thought that maybe there was a file naming error and 
> > renamed a copy of "libesmumps.so" to "libsmumps.so", but then I got a 
> > similar error with a different MUMPS shared object. After a few rounds 
> of 
> > that, I gave up. 
> > 
> > Does anyone know what the issue is and how to solve it? 
> > 
> > Thanks, 
> > Steve 
>

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Re: [deal.II] Installation error using Ubuntu 17.10 package (missing libsmumps.so)

[Matthias Maier]

Hi there,

The problem is that deal.II's CMake system records the full link
interface of all shared libraries - if a library changes location the
package has to be rebuild (in Ubuntu). If this is indeed the case I will
ask for this to happen.

Did you install just the library libdeal.ii, or also the development
package libdeal.ii-dev?

Best,
Matthias



On Thu, Apr 12, 2018, at 13:19 CDT, Stephen DeWitt  wrote:

> Hello all,
> A PRISMS-PF user recently posted to our forum 
>  that 
> he was having an issue with the deal.ii package he got through apt-get on 
> Ubuntu 17.10. The issue seems to be related to a missing shared object file 
> for MUMPS. I booted up a Ubuntu virtual machine on VirtualBox and saw the 
> same error.
>
> What I did:
>
>1. Installed Ubuntu 17.10 on the VM
>2. Updated apt
>3. Retrieved the deal.ii package ($ sudo apt-get install libdeal.ii)
>4. Found the deal.ii example directory to test the installation and 
>copied it into my home directory
>5. Ran CMake for step-1
>6. Attempted to compile step-1 (both "make release" and "make debug" had 
>the same outcome)
>
> The result:
>
> 
>
> I checked the '/usr/lib/' directory and found a number of MUMPS shared 
> objects (libesmumps-5.1.so, libesmumps.a, libesmumps.so, 
> libptesmumps-5.1.so, libptesmumps.a, and libptesmumps.so), but not 
> "libsmumps.so". I thought that maybe there was a file naming error and 
> renamed a copy of "libesmumps.so" to "libsmumps.so", but then I got a 
> similar error with a different MUMPS shared object. After a few rounds of 
> that, I gave up.
>
> Does anyone know what the issue is and how to solve it? 
>
> Thanks,
> Steve

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[deal.II] Installation error using Ubuntu 17.10 package (missing libsmumps.so)

[Stephen DeWitt]

Hello all,
A PRISMS-PF user recently posted to our forum 
 that 
he was having an issue with the deal.ii package he got through apt-get on 
Ubuntu 17.10. The issue seems to be related to a missing shared object file 
for MUMPS. I booted up a Ubuntu virtual machine on VirtualBox and saw the 
same error.

What I did:

   1. Installed Ubuntu 17.10 on the VM
   2. Updated apt
   3. Retrieved the deal.ii package ($ sudo apt-get install libdeal.ii)
   4. Found the deal.ii example directory to test the installation and 
   copied it into my home directory
   5. Ran CMake for step-1
   6. Attempted to compile step-1 (both "make release" and "make debug" had 
   the same outcome)

The result:



I checked the '/usr/lib/' directory and found a number of MUMPS shared 
objects (libesmumps-5.1.so, libesmumps.a, libesmumps.so, 
libptesmumps-5.1.so, libptesmumps.a, and libptesmumps.so), but not 
"libsmumps.so". I thought that maybe there was a file naming error and 
renamed a copy of "libesmumps.so" to "libsmumps.so", but then I got a 
similar error with a different MUMPS shared object. After a few rounds of 
that, I gave up.

Does anyone know what the issue is and how to solve it? 

Thanks,
Steve

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[deal.II] installation error

[Juan Carlos Araujo Cabarcas]

Dear all,

I am trying to install deal.II from the GIT repository with the following 
features:

petsc_ver='3.6.0';
trilinos_ver='12.4.2';

git clone https://github.com/dealii/dealii.git dealii

cmake \
-DTRILINOS_DIR=${install_dir}/trilinos-${trilinos_ver} \
-DP4EST_DIR=${install_dir}/FAST \
-DDEAL_II_WITH_METIS=ON \
-DMETIS_DIR=$METIS_DIR \
-DDEAL_II_WITH_MPI=ON \
-DDEAL_II_WITH_THREADS=OFF \
-DDEAL_II_WITH_UMFPACK=ON \
-DDEAL_II_WITH_LAPACK=ON \
-DDEAL_II_WITH_PETSC=ON \
-DPETSC_ARCH=$PETSC_ARCH \
-DPETSC_DIR=$PETSC_DIR \
-DDEAL_II_WITH_SLEPC=ON \
-DSLEPC_DIR=$SLEPC_DIR \
-DDEAL_II_WITH_P4EST=ON \
-DDEAL_II_WITH_ARPACK=ON \
-DDEAL_II_WITH_TRILINOS=ON \
-DCMAKE_INSTALL_PREFIX=${install_dir}/dealii ${install_dir}/dealii;

make -j${virtual_proc} install;

I get the following installation error:

[ 50%] Building CXX object 
source/fe/CMakeFiles/obj_fe_debug.dir/fe_poly.cc.o
mypath/dealii/source/lac/scalapack.cc: In member function ‘void 
dealii::ScaLAPACKMatrix::copy_to(dealii::ScaLAPACKMatrix&)
 
const’:
mypath/dealii/source/lac/scalapack.cc:243:91: error: there are no arguments 
to ‘MPI_Comm_create_group’ that depend on a template parameter, so a 
declaration of ‘MPI_Comm_create_group’ must be available [-fpermissive]
   ierr = MPI_Comm_create_group(MPI_COMM_WORLD, group_union, 5, 
&mpi_communicator_union);

   
^
mypath/dealii/source/lac/scalapack.cc:243:91: note: (if you use 
‘-fpermissive’, G++ will accept your code, but allowing the use of an 
undeclared name is deprecated)
mypath/dealii/source/lac/scalapack.cc: In instantiation of ‘void 
dealii::ScaLAPACKMatrix::copy_to(dealii::ScaLAPACKMatrix&)
 
const [with NumberType = double]’:
mypath/dealii/source/lac/scalapack.cc:760:16:   required from here
mypath/dealii/source/lac/scalapack.cc:243:91: error: 
‘MPI_Comm_create_group’ was not declared in this scope
mypath/dealii/source/lac/scalapack.cc: In instantiation of ‘void 
dealii::ScaLAPACKMatrix::copy_to(dealii::ScaLAPACKMatrix&)
 
const [with NumberType = float]’:
mypath/dealii/source/lac/scalapack.cc:761:16:   required from here
mypath/dealii/source/lac/scalapack.cc:243:91: error: 
‘MPI_Comm_create_group’ was not declared in this scope
[ 50%] Building CXX object 
source/grid/CMakeFiles/obj_grid_debug.dir/grid_reordering.cc.o
make[2]: *** [source/lac/CMakeFiles/obj_lac_debug.dir/scalapack.cc.o] Error 
1
make[1]: *** [source/lac/CMakeFiles/obj_lac_debug.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs

Last time I had errors was due to Trilinos version, but I updated that one 
to the current in use.
Any ideas for resolving the error?

Aditionally, how can I set from GIT the last stable (tested) version?

Thanks in advance,
Juan Carlos Araújo, 
Umeå Universitet

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[deal.II] Installation error, please help, thx!

[Michael]

Hi,

I've installed dealii before using the default step from README. This time, 
I am trying to install dealii with trilinos, but getting the following kind 
of errors during installation:

"
/usr/include/c++/6/tuple:648:21: error: no type named ‘type’ in ‘struct 
std::enable_if’
 bool>::type=false>
 ^
/usr/include/c++/6/tuple:648:21: note: invalid template non-type parameter
/usr/include/c++/6/tuple:636:19: note: candidate: template, 
std::_Placeholder<1>, std::_Placeholder<2>, float*, std::unique_ptr >, 
std::unique_ptr >, 
std::reference_wrapper >, 
std::reference_wrapper > >::_NotSameTuple<_UElements 
...>() && std::_TC<(8ul == sizeof... (_UElements)), 
std::reference_wrapper, 
std::_Placeholder<1>, std::_Placeholder<2>, float*, std::unique_ptr >, 
std::unique_ptr >, 
std::reference_wrapper >, 
std::reference_wrapper > 
>::_MoveConstructibleTuple<_UElements ...>()) && std::_TC<(8ul == sizeof... 
(_UElements)), std::reference_wrapper, 
std::_Placeholder<1>, std::_Placeholder<2>, float*, std::unique_ptr >, 
std::unique_ptr >, 
std::reference_wrapper >, 
std::reference_wrapper > 
>::_ImplicitlyMoveConvertibleTuple<_UElements ...>()) && (8ul >= 1)), 
bool>::type  > constexpr std::tuple<  
>::tuple(_UElements&& ...)
 constexpr tuple(_UElements&&... __elements)
"

I checked the directory /usr/include/c++/6/ which seems being redirected 
from /usr/include/c++/6.2.0/. The date of directory c++/6 is the date when 
I installed BOOST. Not sure if this information could help. Please let me 
know if you want some cmake output files. Any information from you would be 
helpful, thanks a lot.

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[deal.II] Installation error with c++ lib

[Michael]

Hi,

I've installed dealii before using the default step by README. This time, I 
am trying to install dealii with trilinos, but getting the following kind 
of errors during installation:

"
/usr/include/c++/6/tuple:648:21: error: no type named ‘type’ in ‘struct 
std::enable_if’
 bool>::type=false>
 ^
/usr/include/c++/6/tuple:648:21: note: invalid template non-type parameter
/usr/include/c++/6/tuple:636:19: note: candidate: template, 
std::_Placeholder<1>, std::_Placeholder<2>, float*, std::unique_ptr >, 
std::unique_ptr >, 
std::reference_wrapper >, 
std::reference_wrapper > >::_NotSameTuple<_UElements 
...>() && std::_TC<(8ul == sizeof... (_UElements)), 
std::reference_wrapper, 
std::_Placeholder<1>, std::_Placeholder<2>, float*, std::unique_ptr >, 
std::unique_ptr >, 
std::reference_wrapper >, 
std::reference_wrapper > 
>::_MoveConstructibleTuple<_UElements ...>()) && std::_TC<(8ul == sizeof... 
(_UElements)), std::reference_wrapper, 
std::_Placeholder<1>, std::_Placeholder<2>, float*, std::unique_ptr >, 
std::unique_ptr >, 
std::reference_wrapper >, 
std::reference_wrapper > 
>::_ImplicitlyMoveConvertibleTuple<_UElements ...>()) && (8ul >= 1)), 
bool>::type  > constexpr std::tuple<  
>::tuple(_UElements&& ...)
 constexpr tuple(_UElements&&... __elements)
"

I checked the directory /usr/include/c++/6/ which seems being detected by 
/usr/include/c++/6.2.0/. The date of directory c++/6 is the date when I 
installed BOOST. Not sure if this information could help. Please let me 
know if you want some cmake output files. Any information from you would be 
helpful, thanks a lot.

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Re: [deal.II] Installation error

[Lev Karatun]

Oh, I didn't realize there was a separate page for CMake. Thank you Jean-Paul, 
Wolfgang, the installation completed successfully!

On Tuesday, 27 June 2017 01:13:59 UTC-4, Jean-Paul Pelteret wrote:
>
> Hi Lev,
>
> The information that you were looking for is in the CMake related 
> documentation 
> . You 
> need to pass the
> -DDEAL_II_FORCE_BUNDLED_THREADS=ON
> option at configuration time.
>
> I hope that this helps.
>
> Regards,
> J-P
>
>
> On Tuesday, June 27, 2017 at 6:26:49 AM UTC+2, Lev Karatun wrote:
>>
>> Hi Wolfgang,
>>
>> To be honest I don't think it's described in readme how to use the 
>> bundled version, or at least I couldn't find it. I tried adding the 
>> parameter 
>> -DTBB_INCLUDE_DIR="../bundled/tbb41_20130401oss/include/tbb"
>> but cmake finds the system library at /usr/lib64/libtbb.so and uses it 
>> anyway, and I wasn't able to find the .so file within DealII folder to 
>> specify its location. 
>>
>> Best regards,
>> Lev Karatun.
>>
>> 2017-06-26 22:56 GMT-04:00 Wolfgang Bangerth > >:
>>
>>> On 06/26/2017 10:05 AM, Lev Karatun wrote:
>>>

 #define TBB_VERSION_MAJOR 2
 #define TBB_VERSION_MINOR 2

>>>
>>> That is quite an old version of the TBB. The one we bundle with deal.II 
>>> is 4.1. Can you try to force using the bundled version of the TBB? It 
>>> should be described in doc/readme.html how to do that.
>>>
>>> Best
>>>  W.
>>>
>>> -- 
>>> 
>>> Wolfgang Bangerth  email: bang...@colostate.edu 
>>> 
>>>www: http://www.math.colostate.edu/~bangerth/
>>>
>>>
>>

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Re: [deal.II] Installation error

[Jean-Paul Pelteret]

Hi Lev,

The information that you were looking for is in the CMake related 
documentation 
. You need 
to pass the
-DDEAL_II_FORCE_BUNDLED_THREADS=ON
option at configuration time.

I hope that this helps.

Regards,
J-P


On Tuesday, June 27, 2017 at 6:26:49 AM UTC+2, Lev Karatun wrote:
>
> Hi Wolfgang,
>
> To be honest I don't think it's described in readme how to use the bundled 
> version, or at least I couldn't find it. I tried adding the parameter 
> -DTBB_INCLUDE_DIR="../bundled/tbb41_20130401oss/include/tbb"
> but cmake finds the system library at /usr/lib64/libtbb.so and uses it 
> anyway, and I wasn't able to find the .so file within DealII folder to 
> specify its location. 
>
> Best regards,
> Lev Karatun.
>
> 2017-06-26 22:56 GMT-04:00 Wolfgang Bangerth :
>
>> On 06/26/2017 10:05 AM, Lev Karatun wrote:
>>
>>>
>>> #define TBB_VERSION_MAJOR 2
>>> #define TBB_VERSION_MINOR 2
>>>
>>
>> That is quite an old version of the TBB. The one we bundle with deal.II 
>> is 4.1. Can you try to force using the bundled version of the TBB? It 
>> should be described in doc/readme.html how to do that.
>>
>> Best
>>  W.
>>
>> -- 
>> 
>> Wolfgang Bangerth  email: bange...@colostate.edu
>>www: http://www.math.colostate.edu/~bangerth/
>>
>>
>

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Re: [deal.II] Installation error

[Lev Karatun]

Hi Wolfgang,

To be honest I don't think it's described in readme how to use the bundled
version, or at least I couldn't find it. I tried adding the parameter
-DTBB_INCLUDE_DIR="../bundled/tbb41_20130401oss/include/tbb"
but cmake finds the system library at /usr/lib64/libtbb.so and uses it
anyway, and I wasn't able to find the .so file within DealII folder to
specify its location.

Best regards,
Lev Karatun.

2017-06-26 22:56 GMT-04:00 Wolfgang Bangerth :

> On 06/26/2017 10:05 AM, Lev Karatun wrote:
>
>>
>> #define TBB_VERSION_MAJOR 2
>> #define TBB_VERSION_MINOR 2
>>
>
> That is quite an old version of the TBB. The one we bundle with deal.II is
> 4.1. Can you try to force using the bundled version of the TBB? It should
> be described in doc/readme.html how to do that.
>
> Best
>  W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
>www: http://www.math.colostate.edu/~bangerth/
>
>

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Re: [deal.II] Installation error

[Wolfgang Bangerth]

Lev,

/home/lev/aspect/dealii_debug/source/base/function_parser.cc:478:16:   
required from here
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/bits/stl_construct.h:75:7: 
error: use of deleted function ‘std::unique_ptr<_Tp, _Dp>::unique_ptr(const 
std::unique_ptr<_Tp, _Dp>&) [with _Tp = mu::Parser; _Dp = 
std::default_delete]’

  { ::new(static_cast(__p)) _T1(std::forward<_Args>(__args)...); }
^
In file included from 
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/memory:81:0,
  from 
/home/lev/aspect/dealii_debug/include/deal.II/base/function_parser.h:28,
  from 
/home/lev/aspect/dealii_debug/source/base/function_parser.cc:17:
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/bits/unique_ptr.h:273:7: 
error: declared here

unique_ptr(const unique_ptr&) = delete;
^
make[2]: *** [source/base/CMakeFiles/obj_base_debug.dir/function_parser.cc.o] 


Can you copy the last few lines of errors above the first line you show here? 
I want to see where in this file the problem happens.


Also, what is the compiler and version you use?

Best
 W.


--

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

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[deal.II] Installation error

[Lev Karatun]

Hi,

I'm trying to install the latest version of DealII but get the following 
error:

/home/lev/aspect/dealii_debug/source/base/function_parser.cc:478:16:   
required from here
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/bits/stl_construct.h:75:7: 
error: use of deleted function ‘std::unique_ptr<_Tp, _Dp>::unique_ptr(const 
std::unique_ptr<_Tp, _Dp>&) [with _Tp = mu::Parser; _Dp = 
std::default_delete]’
 { ::new(static_cast(__p)) _T1(std::forward<_Args>(__args)...); }
   ^
In file included from 
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/memory:81:0,
 from 
/home/lev/aspect/dealii_debug/include/deal.II/base/function_parser.h:28,
 from 
/home/lev/aspect/dealii_debug/source/base/function_parser.cc:17:
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/bits/unique_ptr.h:273:7: 
error: declared here
   unique_ptr(const unique_ptr&) = delete;
   ^
make[2]: *** 
[source/base/CMakeFiles/obj_base_debug.dir/function_parser.cc.o] Error 1
make[1]: *** [source/base/CMakeFiles/obj_base_debug.dir/all] Error 2
make: *** [all] Error 2

Could you help me fix it please? 

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Re: [deal.II] Deal.ii installation Error

[RAJAT ARORA]

Hello Timo,

Thanks for the reply. I didn't know about the compilation problems with 
older intel compilers.

Yes, this problem was occurring with intel 2013 update 5 and openmpi 1.7.2

The problem is resolved when I switch to intel 2015 compiler and 
openmpi 1.8.4.

This could be because of the compiler compatibility issue as you mentioned. 

Thanks again.

On Sunday, April 16, 2017 at 6:02:47 PM UTC-4, Timo Heister wrote:
>
> Rajat, 
>
> first, is there a reason you are using deal.II 8.3.0, which is by now 
> to big releases behind? 
> Second, can is there a more modern MPI and compiler you can try? We 
> have had many problems with intel compilers in the past, so I would 
> try a gcc with mpich or openmpi unless you are sure in what you are 
> doing. 
>
> On Sat, Apr 15, 2017 at 5:19 PM, RAJAT ARORA  > wrote: 
> > Hello Everyone, 
> > 
> > I am trying to install deal.ii on Minnesota supercomputing institute 
> using 
> > openmpi compiled with intel. 
> > 
> > However, I am getting several errors during installation. 
> > 
> > I am attaching the install.log file (output of deal.ii installation) 
> since 
> > the errors are huge. 
> > 
> > It starts from line 1878 when the installation reaches 92% during the 
> > compilation of file mapping_fe_field.cc. 
> > 
> > Please help me with the installation. 
> > 
> > Thanks. 
> > 
> > 
> > 
> > -- 
> > The deal.II project is located at 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_&d=DwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=ZzAFG_s-rwwy08oT7yXypuWGWX173CTEdDNsG-y3Yu0&s=SS_oJV8kSW8xkwLez-eSx8Xf5agwsaX8_Zm413D7izU&e=
>  
> > For mailing list/forum options, see 
> > 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_forum_dealii-3Fhl-3Den&d=DwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=ZzAFG_s-rwwy08oT7yXypuWGWX173CTEdDNsG-y3Yu0&s=HYTlTvyBdQWDnTjTrRwi2512DbH-prGRo3eLZECzkhU&e=
>  
> > --- 
> > You received this message because you are subscribed to the Google 
> Groups 
> > "deal.II User Group" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an 
> > email to dealii+un...@googlegroups.com . 
> > For more options, visit 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_optout&d=DwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=ZzAFG_s-rwwy08oT7yXypuWGWX173CTEdDNsG-y3Yu0&s=StK1bh8JvaISuWUcq6kQSHXJOkyulCANz3pb0m7Ge_0&e=
>  
> . 
>
>
>
> -- 
> Timo Heister 
> http://www.math.clemson.edu/~heister/ 
>

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Re: [deal.II] Deal.ii installation Error

[RAJAT ARORA]

Hello Timo,

Thanks for the reply. I didn't know about the compilation problems with 
older intel compilers.

Yes, this problem was occurring with intel 2013 update 5 and openmpi 1.7.2

The problem is resolved when I switch to intel 2015 compiler and 
openmpi 1.8.4.

This could be because of the compiler compatibility issue as you mentioned. 

Thanks again.

On Sunday, April 16, 2017 at 6:02:47 PM UTC-4, Timo Heister wrote:
>
> Rajat, 
>
> first, is there a reason you are using deal.II 8.3.0, which is by now 
> to big releases behind? 
> Second, can is there a more modern MPI and compiler you can try? We 
> have had many problems with intel compilers in the past, so I would 
> try a gcc with mpich or openmpi unless you are sure in what you are 
> doing. 
>
> On Sat, Apr 15, 2017 at 5:19 PM, RAJAT ARORA  > wrote: 
> > Hello Everyone, 
> > 
> > I am trying to install deal.ii on Minnesota supercomputing institute 
> using 
> > openmpi compiled with intel. 
> > 
> > However, I am getting several errors during installation. 
> > 
> > I am attaching the install.log file (output of deal.ii installation) 
> since 
> > the errors are huge. 
> > 
> > It starts from line 1878 when the installation reaches 92% during the 
> > compilation of file mapping_fe_field.cc. 
> > 
> > Please help me with the installation. 
> > 
> > Thanks. 
> > 
> > 
> > 
> > -- 
> > The deal.II project is located at 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_&d=DwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=ZzAFG_s-rwwy08oT7yXypuWGWX173CTEdDNsG-y3Yu0&s=SS_oJV8kSW8xkwLez-eSx8Xf5agwsaX8_Zm413D7izU&e=
>  
> > For mailing list/forum options, see 
> > 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_forum_dealii-3Fhl-3Den&d=DwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=ZzAFG_s-rwwy08oT7yXypuWGWX173CTEdDNsG-y3Yu0&s=HYTlTvyBdQWDnTjTrRwi2512DbH-prGRo3eLZECzkhU&e=
>  
> > --- 
> > You received this message because you are subscribed to the Google 
> Groups 
> > "deal.II User Group" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an 
> > email to dealii+un...@googlegroups.com . 
> > For more options, visit 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_optout&d=DwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=ZzAFG_s-rwwy08oT7yXypuWGWX173CTEdDNsG-y3Yu0&s=StK1bh8JvaISuWUcq6kQSHXJOkyulCANz3pb0m7Ge_0&e=
>  
> . 
>
>
>
> -- 
> Timo Heister 
> http://www.math.clemson.edu/~heister/ 
>

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Re: [deal.II] Deal.ii installation Error

[Timo Heister]

Rajat,

first, is there a reason you are using deal.II 8.3.0, which is by now
to big releases behind?
Second, can is there a more modern MPI and compiler you can try? We
have had many problems with intel compilers in the past, so I would
try a gcc with mpich or openmpi unless you are sure in what you are
doing.

On Sat, Apr 15, 2017 at 5:19 PM, RAJAT ARORA  wrote:
> Hello Everyone,
>
> I am trying to install deal.ii on Minnesota supercomputing institute using
> openmpi compiled with intel.
>
> However, I am getting several errors during installation.
>
> I am attaching the install.log file (output of deal.ii installation) since
> the errors are huge.
>
> It starts from line 1878 when the installation reaches 92% during the
> compilation of file mapping_fe_field.cc.
>
> Please help me with the installation.
>
> Thanks.
>
>
>
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-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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Re: [deal.II] installation Error while installing dealii-8.4.1:/usr/local/lib/liblapack.a: could not read symbols: Bad value

[yoczhang]

Thank you!

在 2016年7月18日星期一 UTC+8下午6:09:19，Matthias Maier写道：
>
>
> > /usr/bin/ld: /usr/local/lib/liblapack.a(sgeev.o): relocation R_X86_64_32 
> > against `.rodata' can not be used when making a shared object; recompile 
> > with -fPIC 
> > /usr/local/lib/liblapack.a: could not read symbols: Bad value 
>
> This means that your local blas and lapack libraries in /usr/local/lib 
> are compiled as an archive without support for "position independent 
> code" (-fpic). 
>
> You have to recompile blas/lapack at least with -fpic, or even better, 
> as a shared library (such that you end up with libblas.so / liblapack.so). 
>
> (To turn off the creation of shared libraries in deal.II via 
> -DBUILD_SHARED_LIBS=OFF is not recommended.) 
>

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Re: [deal.II] installation Error while installing dealii-8.4.1:/usr/local/lib/liblapack.a: could not read symbols: Bad value

[Matthias Maier]

> /usr/bin/ld: /usr/local/lib/liblapack.a(sgeev.o): relocation R_X86_64_32 
> against `.rodata' can not be used when making a shared object; recompile 
> with -fPIC
> /usr/local/lib/liblapack.a: could not read symbols: Bad value

This means that your local blas and lapack libraries in /usr/local/lib
are compiled as an archive without support for "position independent
code" (-fpic).

You have to recompile blas/lapack at least with -fpic, or even better,
as a shared library (such that you end up with libblas.so / liblapack.so).

(To turn off the creation of shared libraries in deal.II via
-DBUILD_SHARED_LIBS=OFF is not recommended.)

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[deal.II] installation Error while installing dealii-8.4.1:/usr/local/lib/liblapack.a: could not read symbols: Bad value

[yoczhang]

while I use the following:
cmake -DCMAKE_INSTALL_PREFIX=/usr/local/dealii/ ../
there was noting wrong message,
but when I make -j2 install, I got the error:
/usr/bin/ld: /usr/local/lib/liblapack.a(sgeev.o): relocation R_X86_64_32 
against `.rodata' can not be used when making a shared object; recompile 
with -fPIC
/usr/local/lib/liblapack.a: could not read symbols: Bad value

thanks for your help!

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