Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

2018-09-19 Thread Sambit Das 
Hi Daniel,

The third issue is fixed in https://github.com/dealii/dealii/pull/7213 
> 
> .

Thank you for creating the fix.


the first issue you observed is related to 
> https://gitlab.kitware.com/cmake/cmake/issues/17538.
> In particular, the MPI include directories might not be set correctly for 
> the CUDA compiler.
> This often happens when the CMAKE_CXX_COMPILER does not need additional 
> include directories to
> compiler MPI code, e.g. if the CMAKE_CXX_COMPILER is a MPI wrapper.

Ah, I see. 

Best,
Sambit
On Wednesday, September 19, 2018 at 4:36:46 AM UTC-5, Daniel Arndt wrote:
>
> Sambit,
>
> the first issue you observed is related to 
> https://gitlab.kitware.com/cmake/cmake/issues/17538.
> In particular, the MPI include directories might not be set correctly for 
> the CUDA compiler.
> This often happens when the CMAKE_CXX_COMPILER does not need additional 
> include directories to
> compiler MPI code, e.g. if the CMAKE_CXX_COMPILER is a MPI wrapper.
>
> The third issue is fixed in https://github.com/dealii/dealii/pull/7213.
>
> Best,
> Daniel
>

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Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

2018-09-19 Thread Daniel Arndt 
Sambit,

the first issue you observed is related to 
https://gitlab.kitware.com/cmake/cmake/issues/17538.
In particular, the MPI include directories might not be set correctly for 
the CUDA compiler.
This often happens when the CMAKE_CXX_COMPILER does not need additional 
include directories to
compiler MPI code, e.g. if the CMAKE_CXX_COMPILER is a MPI wrapper.

The third issue is fixed in https://github.com/dealii/dealii/pull/7213.

Best,
Daniel

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Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

2018-09-18 Thread Sambit Das 
It seems the issue is related to -DDEAL_II_WITH_64BIT_INDICES=ON.
If I set -DDEAL_II_WITH_64BIT_INDICES=OFF, the compilation worked fine.

Best,
Sambit

On Tuesday, September 18, 2018 at 11:17:43 PM UTC-5, Sambit Das wrote:
>
> Hi Bruno and Jean,
>
> Based on the discussion in  (https://github.com/dealii/dealii/issues/7204 
> )
>  
> I used the temporary fix of  setting 
> SET(ZLIB_INCLUDE_DIR  "/usr/local/include") in FindZLIB.cmake, which 
> addressed the above compilation issue.
>
> However, I get a new compilation error now:
>
> *[ 59%] Building CXX object 
> source/particles/CMakeFiles/obj_particle_debug.dir/particle.cc.o*
> */gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/matrix_free/cuda_hanging_nodes_internal.h(286):
>  
> error: no suitable user-defined conversion from "std::vector std::allocator>" to "std::vector std::allocator>" exists*
> *  detected during:*
> *instantiation of "void 
> dealii::CUDAWrappers::internal::HangingNodes::setup_constraints(std::vector  
> int, std::allocator> &, const CellIterator &, unsigned int &) 
> const [with dim=2, 
> CellIterator=dealii::FilteredIterator  
> 2>, false>>>]" *
> */gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/matrix_free/cuda_matrix_free.templates.h(288):
>  
> here*
> *instantiation of "void 
> dealii::CUDAWrappers::internal::ReinitHelper Number>::get_cell_data(const CellFilter &, unsigned int) [with dim=2, 
> Number=float, 
> CellFilter=dealii::FilteredIterator  
> 2>, false>>>]" *
> */gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/matrix_free/cuda_matrix_free.templates.h(578):
>  
> here*
> *instantiation of "void dealii::CUDAWrappers::MatrixFree Number>::reinit(const dealii::Mapping &, const 
> dealii::DoFHandler &, const dealii::AffineConstraints &, 
> const dealii::Quadrature<1> &, dealii::CUDAWrappers::MatrixFree Number>::AdditionalData) [with dim=2, Number=float]" *
> */gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/source/matrix_free/cuda_matrix_free.cu
>  
> (25): here*
>
> The same error occurs with both bundled BOOST as well linking to a 
> manually installed BOOST/1.66.0. 
>
> Do you think the above compilation error is related to the original issue 
> in  (https://github.com/dealii/dealii/issues/7204 
> 
> )?
>
> Thank you,
> Sambit
>
> On Tuesday, September 18, 2018 at 1:02:07 PM UTC-5, Sambit Das wrote:
>>
>> Hi Jean-Paul,
>>
>> Thanks for referring me to the github issue (
>> https://github.com/dealii/dealii/issues/7204 
>> ).
>>  
>> It does seem they are related issues.
>> I will keep following the github issue.
>>
>> Thank you,
>> Sambit
>>
>> On Tuesday, September 18, 2018 at 11:53:17 AM UTC-5, Jean-Paul Pelteret 
>> wrote:
>>>
>>> Hi Sambit,
>>>
>>> Your new error looks like the same one reported (
>>> https://github.com/dealii/dealii/issues/7204 
>>> )
>>>  yesterday 
>>> so I don’t think that using another version of CMake will fix it. I’m not 
>>> quite sure what the answer to the problem is, since the discussion is 
>>> ongoing.
>>>
>>> Best,
>>> Jean-Paul
>>>
>>> On 18 Sep 2018, at 18:47, Sambit Das  wrote:
>>>
>>> Hi Bruno,
>>>
>>> Thank you for your reply. Now I tried CMake 3.9.6 but got the following 
>>> compilation error
>>>
>>> [ 54%] Building CUDA object 
>>> source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
>>> In file included from 
>>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/math_functions.h:8853:0,
>>>  from 
>>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/common_functions.h:257,
>>>  from 
>>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/common_functions.h:50,
>>>  from 
>>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/cuda_runtime.h:115,
>>>  from :0:
>>> /gpfs/gpfs0/software/rhel72/packages/gcc/7.2.0/include/c++/7.2.0/cmath:45:15:
>>>  
>>> fatal error: math.h: No such file or directory
>>>  #include_next 
>>>^~~~
>>> compilation terminated.
>>>
>>> Should I try CMake 3.10/11?
>>>
>>> Thank you,
>>> Sambit
>>>
>>> On Tuesday, September 18, 2018 at 7:27:38 AM UTC-5, Bruno Turcksin wrote:

 Sambit,

 Can you try with a different version of CMake. We do not support CMake 
 3.12 with CUDA at the moment.

 Best,

 Bruno

 On Monday, September 17, 2018 at 8:56:31 PM UTC-4,

Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

2018-09-18 Thread Sambit Das 
Hi Bruno and Jean,

Based on the discussion in  (https://github.com/dealii/dealii/issues/7204 
)
 
I used the temporary fix of  setting 
SET(ZLIB_INCLUDE_DIR  "/usr/local/include") in FindZLIB.cmake, which 
addressed the above compilation issue.

However, I get a new compilation error now:

*[ 59%] Building CXX object 
source/particles/CMakeFiles/obj_particle_debug.dir/particle.cc.o*
*/gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/matrix_free/cuda_hanging_nodes_internal.h(286):
 
error: no suitable user-defined conversion from "std::vector>" to "std::vector>" exists*
*  detected during:*
*instantiation of "void 
dealii::CUDAWrappers::internal::HangingNodes::setup_constraints(std::vector> &, const CellIterator &, unsigned int &) 
const [with dim=2, 
CellIterator=dealii::FilteredIterator, false>>>]" *
*/gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/matrix_free/cuda_matrix_free.templates.h(288):
 
here*
*instantiation of "void 
dealii::CUDAWrappers::internal::ReinitHelper::get_cell_data(const CellFilter &, unsigned int) [with dim=2, 
Number=float, 
CellFilter=dealii::FilteredIterator, false>>>]" *
*/gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/matrix_free/cuda_matrix_free.templates.h(578):
 
here*
*instantiation of "void dealii::CUDAWrappers::MatrixFree::reinit(const dealii::Mapping &, const 
dealii::DoFHandler &, const dealii::AffineConstraints &, 
const dealii::Quadrature<1> &, dealii::CUDAWrappers::MatrixFree::AdditionalData) [with dim=2, Number=float]" *
*/gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/source/matrix_free/cuda_matrix_free.cu(25):
 
here*

The same error occurs with both bundled BOOST as well linking to a manually 
installed BOOST/1.66.0. 

Do you think the above compilation error is related to the original issue 
in  (https://github.com/dealii/dealii/issues/7204 

)?

Thank you,
Sambit

On Tuesday, September 18, 2018 at 1:02:07 PM UTC-5, Sambit Das wrote:
>
> Hi Jean-Paul,
>
> Thanks for referring me to the github issue (
> https://github.com/dealii/dealii/issues/7204 
> ).
>  
> It does seem they are related issues.
> I will keep following the github issue.
>
> Thank you,
> Sambit
>
> On Tuesday, September 18, 2018 at 11:53:17 AM UTC-5, Jean-Paul Pelteret 
> wrote:
>>
>> Hi Sambit,
>>
>> Your new error looks like the same one reported (
>> https://github.com/dealii/dealii/issues/7204 
>> )
>>  yesterday 
>> so I don’t think that using another version of CMake will fix it. I’m not 
>> quite sure what the answer to the problem is, since the discussion is 
>> ongoing.
>>
>> Best,
>> Jean-Paul
>>
>> On 18 Sep 2018, at 18:47, Sambit Das  wrote:
>>
>> Hi Bruno,
>>
>> Thank you for your reply. Now I tried CMake 3.9.6 but got the following 
>> compilation error
>>
>> [ 54%] Building CUDA object 
>> source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
>> In file included from 
>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/math_functions.h:8853:0,
>>  from 
>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/common_functions.h:257,
>>  from 
>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/common_functions.h:50,
>>  from 
>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/cuda_runtime.h:115,
>>  from :0:
>> /gpfs/gpfs0/software/rhel72/packages/gcc/7.2.0/include/c++/7.2.0/cmath:45:15:
>>  
>> fatal error: math.h: No such file or directory
>>  #include_next 
>>^~~~
>> compilation terminated.
>>
>> Should I try CMake 3.10/11?
>>
>> Thank you,
>> Sambit
>>
>> On Tuesday, September 18, 2018 at 7:27:38 AM UTC-5, Bruno Turcksin wrote:
>>>
>>> Sambit,
>>>
>>> Can you try with a different version of CMake. We do not support CMake 
>>> 3.12 with CUDA at the moment.
>>>
>>> Best,
>>>
>>> Bruno
>>>
>>> On Monday, September 17, 2018 at 8:56:31 PM UTC-4, Sambit Das wrote:

 Dear all,

 I am trying to compile the latest development version of dealii 
 (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0, 
 openmpi/3.0.0/gcc/7.2.0,  cuda/9.2 and cmake-3.12.2. 

 During compilation I get the following error:

 [ 57%] Building CUDA object 
 source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
 In file included from

Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

2018-09-18 Thread Sambit Das 
Hi Jean-Paul,

Thanks for referring me to the github issue (
https://github.com/dealii/dealii/issues/7204 
).
 
It does seem they are related issues.
I will keep following the github issue.

Thank you,
Sambit

On Tuesday, September 18, 2018 at 11:53:17 AM UTC-5, Jean-Paul Pelteret 
wrote:
>
> Hi Sambit,
>
> Your new error looks like the same one reported (
> https://github.com/dealii/dealii/issues/7204 
> )
>  yesterday 
> so I don’t think that using another version of CMake will fix it. I’m not 
> quite sure what the answer to the problem is, since the discussion is 
> ongoing.
>
> Best,
> Jean-Paul
>
> On 18 Sep 2018, at 18:47, Sambit Das > 
> wrote:
>
> Hi Bruno,
>
> Thank you for your reply. Now I tried CMake 3.9.6 but got the following 
> compilation error
>
> [ 54%] Building CUDA object 
> source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
> In file included from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/math_functions.h:8853:0,
>  from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/common_functions.h:257,
>  from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/common_functions.h:50,
>  from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/cuda_runtime.h:115,
>  from :0:
> /gpfs/gpfs0/software/rhel72/packages/gcc/7.2.0/include/c++/7.2.0/cmath:45:15: 
> fatal error: math.h: No such file or directory
>  #include_next 
>^~~~
> compilation terminated.
>
> Should I try CMake 3.10/11?
>
> Thank you,
> Sambit
>
> On Tuesday, September 18, 2018 at 7:27:38 AM UTC-5, Bruno Turcksin wrote:
>>
>> Sambit,
>>
>> Can you try with a different version of CMake. We do not support CMake 
>> 3.12 with CUDA at the moment.
>>
>> Best,
>>
>> Bruno
>>
>> On Monday, September 17, 2018 at 8:56:31 PM UTC-4, Sambit Das wrote:
>>>
>>> Dear all,
>>>
>>> I am trying to compile the latest development version of dealii 
>>> (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0, 
>>> openmpi/3.0.0/gcc/7.2.0,  cuda/9.2 and cmake-3.12.2. 
>>>
>>> During compilation I get the following error:
>>>
>>> [ 57%] Building CUDA object 
>>> source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
>>> In file included from 
>>> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/base/cuda.h:19:0,
>>>  from 
>>> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/source/base/
>>> cuda.cu:16:
>>> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/build/include/deal.II/base/config.h:421:12:
>>>  
>>> fatal error: mpi.h: No such file or directory
>>>  #  include 
>>> ^~~
>>> compilation terminated.
>>>
>>>
>>> I have attached the detailed.log file. 
>>>
>>> I have used the following configuration line:
>>> cmake  -DDEAL_II_CXX_FLAGS_RELEASE="-O3" -DDEAL_II_WITH_CXX17=OFF 
>>> -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx 
>>>  -DCMAKE_Fortran_COMPILER=mpif90 -DDEAL_II_WITH_CUDA=ON 
>>> -DDEAL_II_COMPONENT_EXAMPLES=OFF
>>>  -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_64BIT_INDICES=ON
>>>  
>>> -DP4EST_DIR="/gpfs/gpfs0/groups/gavini/dsambit/software/p4est/installGcc7.2.0"
>>>   
>>> ../dealii
>>>
>>>  Interestingly, if I remove -DDEAL_II_WITH_CUDA=ON, compilation is 
>>> successful. I am wondering if I am missing any cuda related compilation 
>>> flags.
>>>
>>> Thanks a lot in advance,
>>>
>>> Best,
>>> Sambit
>>>
>>
> -- 
> 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] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

2018-09-18 Thread Jean-Paul Pelteret 
Hi Sambit,

Your new error looks like the same one reported 
(https://github.com/dealii/dealii/issues/7204 
) yesterday so I don’t think that 
using another version of CMake will fix it. I’m not quite sure what the answer 
to the problem is, since the discussion is ongoing.

Best,
Jean-Paul

> On 18 Sep 2018, at 18:47, Sambit Das  wrote:
> 
> Hi Bruno,
> 
> Thank you for your reply. Now I tried CMake 3.9.6 but got the following 
> compilation error
> 
> [ 54%] Building CUDA object 
> source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
> In file included from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/math_functions.h:8853:0,
>  from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/common_functions.h:257,
>  from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/common_functions.h:50,
>  from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/cuda_runtime.h:115,
>  from :0:
> /gpfs/gpfs0/software/rhel72/packages/gcc/7.2.0/include/c++/7.2.0/cmath:45:15: 
> fatal error: math.h: No such file or directory
>  #include_next 
>^~~~
> compilation terminated.
> 
> Should I try CMake 3.10/11?
> 
> Thank you,
> Sambit
> 
> On Tuesday, September 18, 2018 at 7:27:38 AM UTC-5, Bruno Turcksin wrote:
> Sambit,
> 
> Can you try with a different version of CMake. We do not support CMake 3.12 
> with CUDA at the moment.
> 
> Best,
> 
> Bruno
> 
> On Monday, September 17, 2018 at 8:56:31 PM UTC-4, Sambit Das wrote:
> Dear all,
> 
> I am trying to compile the latest development version of dealii (9.1.0-pre, 
> shortrev c6b7876) using gcc/7.2.0, openmpi/3.0.0/gcc/7.2.0,  cuda/9.2 and 
> cmake-3.12.2. 
> 
> During compilation I get the following error:
> 
> [ 57%] Building CUDA object 
> source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
> In file included from 
> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/base/cuda.h:19:0,
>  from 
> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/source/base/cuda.cu:16
>  :
> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/build/include/deal.II/base/config.h:421:12:
>  fatal error: mpi.h: No such file or directory
>  #  include 
> ^~~
> compilation terminated.
> 
> 
> I have attached the detailed.log file. 
> 
> I have used the following configuration line:
> cmake  -DDEAL_II_CXX_FLAGS_RELEASE="-O3" -DDEAL_II_WITH_CXX17=OFF 
> -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx 
>  -DCMAKE_Fortran_COMPILER=mpif90 -DDEAL_II_WITH_CUDA=ON 
> -DDEAL_II_COMPONENT_EXAMPLES=OFF
>  -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_64BIT_INDICES=ON
>  
> -DP4EST_DIR="/gpfs/gpfs0/groups/gavini/dsambit/software/p4est/installGcc7.2.0"
>   ../dealii
> 
>  Interestingly, if I remove -DDEAL_II_WITH_CUDA=ON, compilation is 
> successful. I am wondering if I am missing any cuda related compilation flags.
> 
> Thanks a lot in advance,
> 
> Best,
> Sambit
> 
> -- 
> The deal.II project is located at http://www.dealii.org/ 
> 
> For mailing list/forum options, see 
> https://groups.google.com/d/forum/dealii?hl=en 
> 
> --- 
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> .
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> .

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