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

2020-11-27 Thread 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,

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

2020-11-26 Thread 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: 
>>>

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

2020-11-26 Thread 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:
>>

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

2020-06-03 Thread Prasad Adhav 
Dear Daniel,

Thank you for your reply.

1. The thing is after I do the cmake step, and go on to do  make --jobs=4
install , I get the following output in the terminal.
make: *** No rule to make target 'install'.  Stop.
Am I running this command from a wrong directory?

2. For the dependencies, should I install them manually? and add them to
cmake command I pass?

Thank you for all the help.
Regards,
Prasad


On Wed, Jun 3, 2020 at 2:39 PM Daniel Arndt  wrote:

> Prasad,
>
> CMake ran successfully and the output looks fine. Some of the example
> steps require certain dependencies which you just didn't activate.
> Note, that you will not be able to use MPI with this configuration.
>
> Best,
> Daniel
>
>
> Am Mi., 3. Juni 2020 um 05:21 Uhr schrieb Prasad Adhav <
> prasada001...@gmail.com>:
>
>> I am sorry to be a bother, but the last time I tried the suggestion
>> without any success.
>> cmake -DDEALII_WITH_MPI=OFF -DDEALII_WITH_TRILINOS=OFF
>> -DDEAL_II_WITH_PETSC=OFF ..
>>
>> I had to shift to a different task.
>>
>> I have to come back to install deal.ii though. I thought of starting a
>> from new.
>> I want to run a coupled simulation using the preCICE library, where
>> deal.ii will be used for FEM part.( hence I am trying to install v9.1.0).
>>
>> I am using Ubuntu 18.04 LTS.
>> cmake version 3.10.2
>>
>> I first did
>> cmake -DCMAKE_INSTALL_PREFIX=/home/prasad/bin/deal.II ../
>>
>> then I did
>> cmake -DDEALII_WITH_MPI=OFF -DDEALII_WITH_TRILINOS=OFF 
>> -DDEAL_II_WITH_PETSC=OFF
>> ..
>>
>> The dealii_cmake.log has the output for my terminal.
>> CMakeError.log and CmakeOutput.log are also attached.
>>
>> The immediate issues seen are
>> -- Include
>> /home/prasad/bin/dealii-9.1.0/cmake/configure/configure_muparser.cmake
>> -- MUPARSER_LIBRARY not found! Call:
>> -- FIND_LIBRARY(MUPARSER_LIBRARY NAMES muparser muparserd HINTS
>> PATH_SUFFIXES lib lib64 lib)
>> -- MUPARSER_INCLUDE_DIR not found! Call:
>> -- FIND_PATH(MUPARSER_INCLUDE_DIR muParserDef.h HINTS PATH_SUFFIXES
>> include)
>> --   MUPARSER_LIBRARIES: *** Required variable "MUPARSER_LIBRARY" set to
>> NOTFOUND ***
>> --   MUPARSER_INCLUDE_DIRS: *** Required variable "MUPARSER_INCLUDE_DIR"
>> set to NOTFOUND ***
>> -- Could NOT find MUPARSER
>> -- DEAL_II_WITH_MUPARSER has unmet external dependencies.
>> -- DEAL_II_WITH_MUPARSER successfully set up with bundled packages.
>>
>>
>> The further output shows, with examples with dependencies not satisfied.
>> -- Configuring done. Proceed to target definitions now.
>> -- Setting up bundled features
>> -- Performing Test DEAL_II_HAVE_FLAG_flifetime_dse=1
>> -- Performing Test DEAL_II_HAVE_FLAG_flifetime_dse=1 - Success
>> -- Performing Test DEAL_II_HAVE_FLAG_Wimplicit_fallthrough=0
>> -- Performing Test DEAL_II_HAVE_FLAG_Wimplicit_fallthrough=0 - Success
>> -- Setting up bundled features - Done
>> -- Setting up library
>> -- Setting up library - Done
>> -- Setting up project configuration
>> -- Setting up project configuration - Done
>> -- Setting up examples
>> --   step-17 - dependencies not satisfied
>> --   step-18 - dependencies not satisfied
>> --   step-32 - dependencies not satisfied
>> --   step-36 - dependencies not satisfied
>> --   step-40 - dependencies not satisfied
>> --   step-42 - dependencies not satisfied
>> --   step-45 - dependencies not satisfied
>> --   step-54 - dependencies not satisfied
>> --   step-55 - dependencies not satisfied
>> --   step-62 - dependencies not satisfied
>> --   step-64 - dependencies not satisfied
>> -- Setting up examples - Done
>> -- Setting up quick_tests in DEBUG mode
>> -- Setting up quick_tests in DEBUG mode - Done
>> -- Setting up testsuite
>> -- Setting up testsuite - Done
>>
>> Thank you in advance for your help and patience.
>>
>> Regards,
>> Prasad ADHAV
>>
>> On Tue, Apr 28, 2020 at 7:09 PM Marc Fehling 
>> wrote:
>>
>>> Hi Prasad!
>>>
>>> My guess now is the following: You have PETSc and Trilinos installed on
>>> your device, which deal.II finds, but complains that PETSc has been
>>> installed with a different MPI configuration as is available for deal.II.
>>>
>>> -- Include
>>> /home/prasad/Downloads/dealii/cmake/configure/configure_3_petsc.cmake
>>> -- Found PETSC_LIBRARY
>>> -- Found PETSC_INCLUDE_DIR_ARCH
>>> -- Found PETSC_INCLUDE_DIR_COMMON
>>> -- PETSC_PETSCVARIABLES not found! Call:
>>> -- FIND_FILE(PETSC_PETSCVARIABLES NAMES petscvariables HINTS
>>> /usr/lib/petscdir/3.6.2//x86_64-linux-gnu-real /usr/lib/petscdir/3.6.2/
>>> PATH_SUFFIXES conf lib/petsc/conf)
>>> --   PETSC_VERSION: 3.7.7.0
>>> --   PETSC_LIBRARIES: /usr/lib/x86_64-linux-gnu/libpetsc.so
>>> --   PETSC_INCLUDE_DIRS: /usr/include/petsc;/usr/include/petsc
>>> --   PETSC_USER_INCLUDE_DIRS: /usr/include/petsc;/usr/include/petsc
>>> -- Found PETSC
>>> -- Could not find a sufficient PETSc installation: PETSc has to be
>>> configured with the same MPI configuration as deal.II.
>>> -- DEAL_II_WITH_PETSC has unmet external dependencies.
>>>
>>> Later, we find:
>>>

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

2020-06-03 Thread Daniel Arndt 
Prasad,

CMake ran successfully and the output looks fine. Some of the example steps
require certain dependencies which you just didn't activate.
Note, that you will not be able to use MPI with this configuration.

Best,
Daniel


Am Mi., 3. Juni 2020 um 05:21 Uhr schrieb Prasad Adhav <
prasada001...@gmail.com>:

> I am sorry to be a bother, but the last time I tried the suggestion
> without any success.
> cmake -DDEALII_WITH_MPI=OFF -DDEALII_WITH_TRILINOS=OFF
> -DDEAL_II_WITH_PETSC=OFF ..
>
> I had to shift to a different task.
>
> I have to come back to install deal.ii though. I thought of starting a
> from new.
> I want to run a coupled simulation using the preCICE library, where
> deal.ii will be used for FEM part.( hence I am trying to install v9.1.0).
>
> I am using Ubuntu 18.04 LTS.
> cmake version 3.10.2
>
> I first did
> cmake -DCMAKE_INSTALL_PREFIX=/home/prasad/bin/deal.II ../
>
> then I did
> cmake -DDEALII_WITH_MPI=OFF -DDEALII_WITH_TRILINOS=OFF 
> -DDEAL_II_WITH_PETSC=OFF
> ..
>
> The dealii_cmake.log has the output for my terminal.
> CMakeError.log and CmakeOutput.log are also attached.
>
> The immediate issues seen are
> -- Include
> /home/prasad/bin/dealii-9.1.0/cmake/configure/configure_muparser.cmake
> -- MUPARSER_LIBRARY not found! Call:
> -- FIND_LIBRARY(MUPARSER_LIBRARY NAMES muparser muparserd HINTS
> PATH_SUFFIXES lib lib64 lib)
> -- MUPARSER_INCLUDE_DIR not found! Call:
> -- FIND_PATH(MUPARSER_INCLUDE_DIR muParserDef.h HINTS PATH_SUFFIXES
> include)
> --   MUPARSER_LIBRARIES: *** Required variable "MUPARSER_LIBRARY" set to
> NOTFOUND ***
> --   MUPARSER_INCLUDE_DIRS: *** Required variable "MUPARSER_INCLUDE_DIR"
> set to NOTFOUND ***
> -- Could NOT find MUPARSER
> -- DEAL_II_WITH_MUPARSER has unmet external dependencies.
> -- DEAL_II_WITH_MUPARSER successfully set up with bundled packages.
>
>
> The further output shows, with examples with dependencies not satisfied.
> -- Configuring done. Proceed to target definitions now.
> -- Setting up bundled features
> -- Performing Test DEAL_II_HAVE_FLAG_flifetime_dse=1
> -- Performing Test DEAL_II_HAVE_FLAG_flifetime_dse=1 - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wimplicit_fallthrough=0
> -- Performing Test DEAL_II_HAVE_FLAG_Wimplicit_fallthrough=0 - Success
> -- Setting up bundled features - Done
> -- Setting up library
> -- Setting up library - Done
> -- Setting up project configuration
> -- Setting up project configuration - Done
> -- Setting up examples
> --   step-17 - dependencies not satisfied
> --   step-18 - dependencies not satisfied
> --   step-32 - dependencies not satisfied
> --   step-36 - dependencies not satisfied
> --   step-40 - dependencies not satisfied
> --   step-42 - dependencies not satisfied
> --   step-45 - dependencies not satisfied
> --   step-54 - dependencies not satisfied
> --   step-55 - dependencies not satisfied
> --   step-62 - dependencies not satisfied
> --   step-64 - dependencies not satisfied
> -- Setting up examples - Done
> -- Setting up quick_tests in DEBUG mode
> -- Setting up quick_tests in DEBUG mode - Done
> -- Setting up testsuite
> -- Setting up testsuite - Done
>
> Thank you in advance for your help and patience.
>
> Regards,
> Prasad ADHAV
>
> On Tue, Apr 28, 2020 at 7:09 PM Marc Fehling 
> wrote:
>
>> Hi Prasad!
>>
>> My guess now is the following: You have PETSc and Trilinos installed on
>> your device, which deal.II finds, but complains that PETSc has been
>> installed with a different MPI configuration as is available for deal.II.
>>
>> -- Include
>> /home/prasad/Downloads/dealii/cmake/configure/configure_3_petsc.cmake
>> -- Found PETSC_LIBRARY
>> -- Found PETSC_INCLUDE_DIR_ARCH
>> -- Found PETSC_INCLUDE_DIR_COMMON
>> -- PETSC_PETSCVARIABLES not found! Call:
>> -- FIND_FILE(PETSC_PETSCVARIABLES NAMES petscvariables HINTS
>> /usr/lib/petscdir/3.6.2//x86_64-linux-gnu-real /usr/lib/petscdir/3.6.2/
>> PATH_SUFFIXES conf lib/petsc/conf)
>> --   PETSC_VERSION: 3.7.7.0
>> --   PETSC_LIBRARIES: /usr/lib/x86_64-linux-gnu/libpetsc.so
>> --   PETSC_INCLUDE_DIRS: /usr/include/petsc;/usr/include/petsc
>> --   PETSC_USER_INCLUDE_DIRS: /usr/include/petsc;/usr/include/petsc
>> -- Found PETSC
>> -- Could not find a sufficient PETSc installation: PETSc has to be
>> configured with the same MPI configuration as deal.II.
>> -- DEAL_II_WITH_PETSC has unmet external dependencies.
>>
>> Later, we find:
>>
>> -- Include
>> /home/prasad/Downloads/dealii/cmake/configure/configure_p4est.cmake
>> -- DEAL_II_WITH_P4EST has unmet configuration requirements:
>> DEAL_II_WITH_MPI has to be set to "ON".
>> --
>> -- Include
>> /home/prasad/Downloads/dealii/cmake/configure/configure_scalapack.cmake
>> -- DEAL_II_WITH_SCALAPACK has unmet configuration requirements:
>> DEAL_II_WITH_MPI has to be set to "ON".
>> --
>> -- Include
>> /home/prasad/Downloads/dealii/cmake/configure/configure_slepc.cmake
>> -- DEAL_II_WITH_SLEPC has unmet configuration requirements:
>> DEAL_II_WITH_PETSC has to be set to "ON".
>>

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

2020-04-28 Thread Marc Fehling 
Hi Prasad!

My guess now is the following: You have PETSc and Trilinos installed on 
your device, which deal.II finds, but complains that PETSc has been 
installed with a different MPI configuration as is available for deal.II.

-- Include 
/home/prasad/Downloads/dealii/cmake/configure/configure_3_petsc.cmake
-- Found PETSC_LIBRARY
-- Found PETSC_INCLUDE_DIR_ARCH
-- Found PETSC_INCLUDE_DIR_COMMON
-- PETSC_PETSCVARIABLES not found! Call:
-- FIND_FILE(PETSC_PETSCVARIABLES NAMES petscvariables HINTS 
/usr/lib/petscdir/3.6.2//x86_64-linux-gnu-real /usr/lib/petscdir/3.6.2/ 
PATH_SUFFIXES conf lib/petsc/conf)
--   PETSC_VERSION: 3.7.7.0
--   PETSC_LIBRARIES: /usr/lib/x86_64-linux-gnu/libpetsc.so
--   PETSC_INCLUDE_DIRS: /usr/include/petsc;/usr/include/petsc
--   PETSC_USER_INCLUDE_DIRS: /usr/include/petsc;/usr/include/petsc
-- Found PETSC
-- Could not find a sufficient PETSc installation: PETSc has to be 
configured with the same MPI configuration as deal.II.
-- DEAL_II_WITH_PETSC has unmet external dependencies.

Later, we find:

-- Include 
/home/prasad/Downloads/dealii/cmake/configure/configure_p4est.cmake
-- DEAL_II_WITH_P4EST has unmet configuration requirements: 
DEAL_II_WITH_MPI has to be set to "ON".
-- 
-- Include 
/home/prasad/Downloads/dealii/cmake/configure/configure_scalapack.cmake
-- DEAL_II_WITH_SCALAPACK has unmet configuration requirements: 
DEAL_II_WITH_MPI has to be set to "ON".
-- 
-- Include 
/home/prasad/Downloads/dealii/cmake/configure/configure_slepc.cmake
-- DEAL_II_WITH_SLEPC has unmet configuration requirements: 
DEAL_II_WITH_PETSC has to be set to "ON".

Is your intention to use parallel features of deal.II? Otherwise I'd 
suggest to explicitly disable all parallel features for now with:
cmake -DDEALII_WITH_MPI=OFF -DDEALII_WITH_TRILINOS=OFF 
-DDEAL_II_WITH_PETSC=OFF ..

Hope this helps for now!

Best,
Marc

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

2020-04-28 Thread Prasad Adhav 
Marc,

I hope this helps with figuring out the failing test.
Thank you very much for your help.

Regards,
Prasad

On Tue, Apr 28, 2020 at 4:04 PM Marc Fehling 
wrote:

> Prasad!
>
> If you look closely into your CMakeError.log file, you'll find that there
> are multiple tests failing. This is not a bad thing: deal.II figures out
> your system configuration this way and enables/disables certain features.
> However in your case, it seems that there is a mandatory test failing, and
> I can not figure out which one by these two log files alone. Could you
> provide your cmake console output?
>
> Could you redirect your console output into a file e.g. via `cmake .. >
> console.log` and forward it?
>
> Best,
> Marc
>
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> 
> .
>


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prasada001...@gmail.com

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-- This is CMake 3.10.2
-- 
-- Include /home/prasad/Downloads/dealii/cmake/setup_external_macros.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_add_flags.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_check_compiler_setup.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_check_cxx_compiler_bug.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_check_mpi_interface.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_clear_cmake_required.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_configure_feature.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_deal_ii_add_definitions.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_deal_ii_add_library.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_deal_ii_add_test.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_deal_ii_find_file.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_deal_ii_find_library.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_deal_ii_find_path.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_deal_ii_find_program.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_deal_ii_initialize_cached_variables.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_deal_ii_insource_setup_target.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_deal_ii_invoke_autopilot.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_deal_ii_package_handle.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_deal_ii_pickup_tests.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_deal_ii_query_git_information.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_deal_ii_setup_target.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_decorate_with_stars.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_enable_if_links.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_enable_if_supported.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_enable_language_optional.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_evaluate_expression.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_expand_instantiations.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_filter_system_libraries.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_find_package.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_find_system_library.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_item_matches.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_purge_feature.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_register_feature.cmake
-- Include /home/prasad/Downloads/dealii/cmake/macros/macro_remove_duplicates.cmake
-- Include

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

2020-04-28 Thread Marc Fehling 
Prasad!

If you look closely into your CMakeError.log file, you'll find that there 
are multiple tests failing. This is not a bad thing: deal.II figures out 
your system configuration this way and enables/disables certain features. 
However in your case, it seems that there is a mandatory test failing, and 
I can not figure out which one by these two log files alone. Could you 
provide your cmake console output?

Could you redirect your console output into a file e.g. via `cmake .. > 
console.log` and forward it?

Best,
Marc

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

2020-04-28 Thread Marc Fehling 
Hi Prasad!

On Tuesday, April 28, 2020 at 10:54:54 AM UTC+2, Prasad Adhav wrote:
>
> I am using cmake version 3.10.2
>

With version 3.10.2, it is less likely that my suggestion will fix your 
problem.

Did cmake actually finished the configuration, as Wolfgang pointed out? 
Going through the error log, you may not have all dependencies of deal.II 
fulfilled, and I'm not entirely sure which tests are mandatory to pass. 
What does cmake print in your console when you run `cmake ..`? The end of 
the console output should give you a hint on what's missing.

Best,
Marc

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

2020-04-28 Thread Prasad Adhav 
Hello Marc,

Thank you for your reply.
I am using cmake version 3.10.2
My OS is Ubuntu 18.04 LTS.

Do you think the cmake version is an issue?
I will try the fix from the issue you suggested.

Regards,
Prasad

On Tue, Apr 28, 2020 at 10:47 AM Marc Fehling 
wrote:

> Hi Prasad!
>
> Thank you for providing the logs! It seems like this here is the cause of
> it:
>
> /usr/bin/ld: cannot find -lpthreads
>
>
> It seems like this is again related to the `-lpthread` problem. Just out
> of curiosity: Which version of cmake and which OS are you using? They may
> have updated CMake in their repository which could be the reason why we see
> this issue more frequently recently...
>
> This may have been fixed upstream in pull request #9117
> . This issue only occurs
> with CMake version >= 3.16. Just compile from the master branch and you
> should be good!
>
> Best,
> Marc
>
> On Monday, April 27, 2020 at 11:27:31 AM UTC+2, Prasad Adhav wrote:
>>
>> Hello,
>>
>> I am trying to install deal.ii for the first time.
>> I followed the instructions on the readme page(
>> https://www.dealii.org/current/readme.html)
>>
>> I use the following for cmake and it worked fine:
>>
>> prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ cmake
>> -DCMAKE_INSTALL_PREFIX=/home/
>> prasad/Downloads/dealii-9.1.1/dealii_install/ ..
>>
>> Then I tried to do `make`, `make info` and `make install`, I get a
>> similar error as follows:
>> prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ make info
>> make: *** No rule to make target 'info'.  Stop.
>>
>> prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ make install
>> make: *** No rule to make target 'install'.  Stop.
>>
>> I apologize if this was already posted, in my search I did not find any
>> questions similar to this.
>> Can anyone help with this?
>> Thank you.
>>
>>
>>
>> --
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> 
> .
>


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Prasad ADHAV
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Re: [deal.II] Re: Deal.ii installation

2020-04-28 Thread Prasad Adhav 
Hello Wilmar,

I did install cmake for another library I am using.
The installation worked and I have tested out those installations.

On Mon, Apr 27, 2020 at 8:18 PM Wilmar Alves Cruvinel Lima <
wilmar84018...@gmail.com> wrote:

>
>
> Em segunda-feira, 27 de abril de 2020 06:27:31 UTC-3, Prasad Adhav
> escreveu:
>>
>> Hello,
>>
>> I am trying to install deal.ii for the first time.
>> I followed the instructions on the readme page(
>> https://www.dealii.org/current/readme.html)
>>
>> I use the following for cmake and it worked fine:
>>
>> prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ cmake
>> -DCMAKE_INSTALL_PREFIX=/home/
>> prasad/Downloads/dealii-9.1.1/dealii_install/ ..
>>
>> Then I tried to do `make`, `make info` and `make install`, I get a
>> similar error as follows:
>> prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ make info
>> make: *** No rule to make target 'info'.  Stop.
>>
>> prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ make install
>> make: *** No rule to make target 'install'.  Stop.
>>
>> I apologize if this was already posted, in my search I did not find any
>> questions similar to this.
>> Can anyone help with this?
>> Thank you.
>>
>> Hi, Prasad,
>>
>
> I am installing Dealii too. I apologise by not have the solution, but I
> want to ask you if you first installed Cmake and begin using it. You didn't
> do that?
>
> Thank you.
>
> Wilmar.
>
>
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> 
> .
>


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Re: [deal.II] Re: deal.II installation on cray XC50 giving MPI_VERSION=0.0

2020-02-10 Thread Wolfgang Bangerth 

On 2/7/20 11:43 PM, vachan potluri wrote:
I really appreciate and value your involvement in this thread. I have 
attached mpi.h with this mail. I want to mention that I added this line 
in FindMPI.cmake just before DEAL_II_FIND_FILE(MPI_MPI_H ...):

MESSAGE(STATUS "Searching for mpi.h in ${MPI_CXX_INCLUDE_PATH}")
and found the corresponding output by cmake to be as follows.
-- Include 
/home/ComptGasDynLab/vachanpotluri/source/dealii-9.1.1/cmake/configure/configure_1_mpi.cmake

-- Searching for mpi.h in
-- Found MPI_MPI_H
--   MPI_VERSION: 3.1
--   MPI_LIBRARIES:
--   MPI_INCLUDE_DIRS:
--   MPI_USER_INCLUDE_DIRS:
--   MPI_CXX_FLAGS:
--   MPI_LINKER_FLAGS:
-- Found MPI
-- DEAL_II_WITH_MPI successfully set up with external dependencies.
Notice that the path is not printed, the variable is empty! Probably the 
problem is not with reading the header but with the variable being 
changed somewhere else.


Yes, this is how it looks like. But Then it seems to have found mpi.h 
anyway, in the next line -- wasn't the original problem that it didn't 
find the file?




It's still possible that everything links correctly. What happens if
you run
cmake and then compile? Does it work? 

I have not tried compiling the source because there are some other 
things also that I wanted to figure out.


As I mentioned before, I don't think that the failed detection of the 
MPI version has any practical effect as long as compiling and linking 
succeeds and unless you want to run on many thousands of nodes.


Best
 W.

--

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

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