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 <petscvec.h>
      |            ^~~~~~~~~~~~
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 <petscvec.h>
      |            ^~~~~~~~~~~~
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 <petscvec.h>
      |            ^~~~~~~~~~~~
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 <petscsys.h>
      |            ^~~~~~~~~~~~
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 <petscvec.h>
      |            ^~~~~~~~~~~~
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 <petsc.h>
      |            ^~~~~~~~~
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 file or directory
   32 | #  include <petscvec.h>
      |            ^~~~~~~~~~~~
compilation terminated.
make[2]: *** [source/distributed/CMakeFiles/obj_distributed_debug.dir/build.make:95: source/distributed/CMakeFiles/obj_distributed_debug.dir/solution_transfer.cc.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 50%] Building CXX object source/matrix_free/CMakeFiles/obj_matrix_free_debug.dir/mapping_info.cc.o
In file included from /home/pushkar/dealii-9.0.0/source/fe/fe_abf.cc:28:
/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 <petsc.h>
      |            ^~~~~~~~~
compilation terminated.
make[2]: *** [source/fe/CMakeFiles/obj_fe_debug.dir/build.make:108: source/fe/CMakeFiles/obj_fe_debug.dir/fe_abf.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:3480: source/fe/CMakeFiles/obj_fe_debug.dir/all] Error 2
[ 50%] Building CXX object source/matrix_free/CMakeFiles/obj_matrix_free_debug.dir/matrix_free.cc.o
In file included from /home/pushkar/dealii-9.0.0/include/deal.II/matrix_free/mapping_info.templates.h:24,
                 from /home/pushkar/dealii-9.0.0/source/matrix_free/mapping_info.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 <petsc.h>
      |            ^~~~~~~~~
compilation terminated.
make[2]: *** [source/matrix_free/CMakeFiles/obj_matrix_free_debug.dir/build.make:95: source/matrix_free/CMakeFiles/obj_matrix_free_debug.dir/mapping_info.cc.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 50%] Building CXX object source/grid/CMakeFiles/obj_grid_debug.dir/grid_generator.cc.o
[ 50%] Building CXX object source/grid/CMakeFiles/obj_grid_debug.dir/grid_in.cc.o
make[1]: *** [CMakeFiles/Makefile2:3696: source/base/CMakeFiles/obj_base_debug.dir/all] Error 2
[ 50%] Building CXX object source/grid/CMakeFiles/obj_grid_debug.dir/grid_out.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/grid/grid_out.cc:27:
/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 <petsc.h>
      |            ^~~~~~~~~
compilation terminated.
make[2]: *** [source/grid/CMakeFiles/obj_grid_debug.dir/build.make:121: source/grid/CMakeFiles/obj_grid_debug.dir/grid_out.cc.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 50%] Building CXX object source/hp/CMakeFiles/obj_hp_debug.dir/dof_level.cc.o
[ 50%] Building CXX object source/hp/CMakeFiles/obj_hp_debug.dir/fe_collection.cc.o
[ 50%] Built target obj_gmsh_debug
[ 50%] Building CXX object source/hp/CMakeFiles/obj_hp_debug.dir/fe_values.cc.o
[ 51%] Building CXX object source/hp/CMakeFiles/obj_hp_debug.dir/mapping_collection.cc.o
[ 51%] Building CXX object source/hp/CMakeFiles/obj_hp_debug.dir/dof_handler.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/source/hp/fe_values.cc:16:
/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 <petsc.h>
      |            ^~~~~~~~~
compilation terminated.
 The above out isnt the complete output but only the eror part in the output and I eventually ended with make error . Moreover,I have compiled deal.II with Trilinos ,Petsc ,p4est,cuda and mpi flags "on". Any header in this regard is appreciated .

Regards

Pushkar

[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

[Pushkar Pandit]

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

--
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+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/2e2fb11a-c1b9-4ef6-9158-9373f134a40cn%40googlegroups.com.

[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

[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

To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/66f6b7a8-30d4-4aac-8482-3e1f00b3f303n%40googlegroups.com.