Re: [deal.II] Re: cmake fails when -DDEAL_II_WITH_MPI=ON

2018-01-25 Thread Eldar Khattatov 
I tried both development and 8.5.1 as I found a discussion about changes in 
MPI configuration somewhere in deal.ii github page.
Thank you for pointing me to these lines in the error log, I will try to 
look into that.

On Thursday, January 25, 2018 at 4:17:26 PM UTC-5, Wolfgang Bangerth wrote:
>
> On 01/25/2018 12:32 PM, Eldar Khattatov wrote: 
> > Sorry that was indeed a wrong file. I attached the right one. 
>
> I *think* the problem comes from the this error: 
>
> /usr/bin/c++   [...] 
> /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so: error: undefined 
> reference to 'opal_uses_threads' 
> /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so: error: undefined 
> reference to 'opal_class_initialize' 
> /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so: error: undefined 
> reference to 'opal_list_item_t_class' 
> collect2: error: ld returned 1 exit status 
> CMakeFiles/cmTC_48103.dir/build.make:130: recipe for target 'cmTC_48103' 
> failed 
> make[1]: *** [cmTC_48103] Error 1 
> make[1]: Leaving directory 
> '/home/username/Downloads/dealii/build/CMakeFiles/CMakeTmp' 
> Makefile:126: recipe for target 'cmTC_48103/fast' failed 
> make: *** [cmTC_48103/fast] Error 2 
>
> Source file was: 
> int main(){ return 0; } 
>
>
> Here, you are using the regular C++ compiler to link an MPI program, and 
> it forgets to link in one of the ancillary OpenMPI libraries that has 
> the opal_... functions. You ought to be using the mpic++ program to 
> compile. Do you have the CXX environment variable set? 
>
> There have been recent changes to the MPI cmake configuration. Are you 
> using the newest development version of deal.II? 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>

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Re: [deal.II] Re: cmake fails when -DDEAL_II_WITH_MPI=ON

2018-01-25 Thread Wolfgang Bangerth 

On 01/25/2018 12:32 PM, Eldar Khattatov wrote:

Sorry that was indeed a wrong file. I attached the right one.


I *think* the problem comes from the this error:

/usr/bin/c++   [...]
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so: error: undefined 
reference to 'opal_uses_threads'
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so: error: undefined 
reference to 'opal_class_initialize'
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so: error: undefined 
reference to 'opal_list_item_t_class'

collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_48103.dir/build.make:130: recipe for target 'cmTC_48103' 
failed

make[1]: *** [cmTC_48103] Error 1
make[1]: Leaving directory 
'/home/username/Downloads/dealii/build/CMakeFiles/CMakeTmp'

Makefile:126: recipe for target 'cmTC_48103/fast' failed
make: *** [cmTC_48103/fast] Error 2

Source file was:
int main(){ return 0; }


Here, you are using the regular C++ compiler to link an MPI program, and 
it forgets to link in one of the ancillary OpenMPI libraries that has 
the opal_... functions. You ought to be using the mpic++ program to 
compile. Do you have the CXX environment variable set?


There have been recent changes to the MPI cmake configuration. Are you 
using the newest development version of deal.II?


Best
 W.

--

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

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Re: [deal.II] Re: cmake fails when -DDEAL_II_WITH_MPI=ON

2018-01-25 Thread Eldar Khattatov 
Sorry that was indeed a wrong file. I attached the right one.

On Thursday, January 25, 2018 at 11:25:21 AM UTC-5, Eldar Khattatov wrote:
>
> Hi,
>
> Thank you for the reply.
> I attached the cmake log file.
>
> On Wednesday, January 24, 2018 at 11:35:53 PM UTC-5, Matthias Maier wrote:
>>
>> Hi, 
>>
>> On Wed, Jan 24, 2018, at 11:17 CST, Eldar Khattatov  
>> wrote: 
>>
>> > I forgot to mention, I tried both the development and 8.5.1versions of 
>> > deal.II and the errors are the same. 
>>
>> The test in question tries to compile a very minimalistic 
>>
>>   int main () { return 0; } 
>>
>> with the given compiler, link interface and linker options. 
>>
>> Have a look at /CMakeFiles/CMakeErrors.log the detailed 
>> compiler output of what exactly fails should be at the very bottom. 
>>
>> I am curious what is going wrong. 
>>
>> Best, 
>> Matthias 
>>
>

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Performing C++ SOURCE FILE Test DEAL_II_HAVE_AVX failed with the following 
output:
Change Dir: /home/username/Downloads/dealii/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_ef482/fast"
/usr/bin/make -f CMakeFiles/cmTC_ef482.dir/build.make 
CMakeFiles/cmTC_ef482.dir/build
make[1]: Entering directory 
'/home/username/Downloads/dealii/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_ef482.dir/src.cxx.o
/usr/bin/c++-DDEAL_II_HAVE_AVX   -o CMakeFiles/cmTC_ef482.dir/src.cxx.o -c 
/home/username/Downloads/dealii/build/CMakeFiles/CMakeTmp/src.cxx
/home/username/Downloads/dealii/build/CMakeFiles/CMakeTmp/src.cxx:3:6: error: 
#error "__AVX__ flag not set, no support for AVX"
 #error "__AVX__ flag not set, no support for AVX"
  ^
/home/username/Downloads/dealii/build/CMakeFiles/CMakeTmp/src.cxx: In function 
‘int main()’:
/home/username/Downloads/dealii/build/CMakeFiles/CMakeTmp/src.cxx:35:9: 
warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi]
   b = _mm256_set1_pd ((volatile double)(2.25));
   ~~^~
CMakeFiles/cmTC_ef482.dir/build.make:65: recipe for target 
'CMakeFiles/cmTC_ef482.dir/src.cxx.o' failed
make[1]: *** [CMakeFiles/cmTC_ef482.dir/src.cxx.o] Error 1
make[1]: Leaving directory 
'/home/username/Downloads/dealii/build/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_ef482/fast' failed
make: *** [cmTC_ef482/fast] Error 2

Return value: 1
Source file was:

#ifndef __AVX__
#error "__AVX__ flag not set, no support for AVX"
#endif
#include 
class VectorizedArray
{
public:
  VectorizedArray &
  operator += (const VectorizedArray )
  {
data = _mm256_add_pd (data, vec.data);
return *this;
  }
  __m256d data;
};
inline
VectorizedArray
operator + (const VectorizedArray , const VectorizedArray )
{
  VectorizedArray tmp = u;
  return tmp+=v;
}
int main()
{
  __m256d a, b;
  const unsigned int vector_bytes = sizeof(__m256d);
  const int n_vectors = vector_bytes/sizeof(double);
  __m256d * data =
reinterpret_cast<__m256d*>(_mm_malloc (2*vector_bytes, vector_bytes));
  double * ptr = reinterpret_cast();
  ptr[0] = (volatile double)(1.0);
  for (int i=1; i([1]);
  unsigned int return_value = 0;
  if (ptr[0] != 7.3125)
return_value = 1;
  for (int i=1; i();
  for (int i=0; i

Re: [deal.II] Re: cmake fails when -DDEAL_II_WITH_MPI=ON

2018-01-25 Thread Matthias Maier 
Hi,

is this really the CMakeError.log for the failing configuration (when
MPI is enabled)?

You should have a failing test right at the end with

  Performing C++ SOURCE FILE Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG failed with 
the following output:

  [...]

  Source file was:
  int main(){ return 0; }

Best,
Matthias

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Re: [deal.II] Re: cmake fails when -DDEAL_II_WITH_MPI=ON

2018-01-24 Thread Matthias Maier 
Hi,

On Wed, Jan 24, 2018, at 11:17 CST, Eldar Khattatov  
wrote:

> I forgot to mention, I tried both the development and 8.5.1versions of 
> deal.II and the errors are the same.

The test in question tries to compile a very minimalistic

  int main () { return 0; }

with the given compiler, link interface and linker options.

Have a look at /CMakeFiles/CMakeErrors.log the detailed
compiler output of what exactly fails should be at the very bottom.

I am curious what is going wrong.

Best,
Matthias

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[deal.II] Re: cmake fails when -DDEAL_II_WITH_MPI=ON

2018-01-24 Thread Eldar Khattatov 
I forgot to mention, I tried both the development and 8.5.1versions of 
deal.II and the errors are the same.

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