Hi,
You can use FFTW 3.3.9, but Intel MKL FFT (cmake -DMKLFFT=ON) is
much faster on Intel CPUs.
Best regards,
Takanori Nakane
On 2021/09/12 0:48, Hoover, David (NIH/CIT) [E] wrote:
> Gotcha.
>
> However, fftw 3.3.8 will not compile with our latest version of intel. fftw 3.3.9 will, though. Can we substitute fftw versions?
>
> David
>
> On 9/10/2021 6:33 PM, Takanori Nakane wrote:
>> Hi,
>>
>> The latest version of the Intel compiler is available for free
>> (even to commercial users) as part of the Intel oneAPI HPC SDK.
>> https://software.intel.com/content/www/us/en/develop/tools/oneapi/all-toolkits.html
>>
>> For compilation, are you aware that you must use
>> cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc?
>> CC and CXX environmental variables are no longer supported in RELION.
>>
>> https://relion.readthedocs.io/en/latest/Installation.html
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>> On 2021/09/11 1:39, Hoover, David (NIH/CIT) [E] wrote:
>>> What is the optimal version of intel compilers for RELION with CPU acceleration?
>>>
>>> I am seeing errors when attempting to compile RELION/3.1.3 with Intel/2019.4.243:
>>>
>>> [ 58%] Linking CXX executable ../../bin/relion_refine_mpi
>>> ../../lib/librelion_lib.a(ml_optimiser_mpi.cpp.o): In function `void tbb::interface7::task_arena::execute_impl<void,
>>> tbb::flow::interface10::graph::wait_functor const>(tbb::flow::interface10::graph::wait_functor const&)':
>>> /usr/local/intel/compilers_and_libraries_2019.4.243/linux/tbb/include/tbb/task_arena.h:213: undefined reference to
>>> `tbb::interface7::internal::task_arena_base::internal_execute(tbb::interface7::internal::delegate_base&) const'
>>> ../../lib/librelion_lib.a(ml_optimiser_mpi.cpp.o): In function `tbb::interface7::task_arena::terminate()':
>>> /usr/local/intel/compilers_and_libraries_2019.4.243/linux/tbb/include/tbb/task_arena.h:281: undefined reference to
>>> `tbb::interface7::internal::task_arena_base::internal_terminate()'
>>> ../../lib/librelion_lib.a(ml_optimiser_mpi.cpp.o): In function `tbb::interface7::task_arena::initialize()':
>>> /usr/local/intel/compilers_and_libraries_2019.4.243/linux/tbb/include/tbb/task_arena.h:250: undefined reference to
>>> `tbb::interface7::internal::task_arena_base::internal_initialize()'
>>> ../../lib/librelion_lib.a(ml_optimiser_mpi.cpp.o): In function `void tbb::interface7::task_arena::execute_impl<void,
>>> tbb::flow::interface10::graph::wait_functor const>(tbb::flow::interface10::graph::wait_functor const&)':
>>> /usr/local/intel/compilers_and_libraries_2019.4.243/linux/tbb/include/tbb/task_arena.h:213: undefined reference to
>>> `tbb::interface7::internal::task_arena_base::internal_execute(tbb::interface7::internal::delegate_base&) const'
>>> ../../lib/librelion_lib.a(ml_optimiser_mpi.cpp.o): In function `tbb::interface7::task_arena::terminate()':
>>> /usr/local/intel/compilers_and_libraries_2019.4.243/linux/tbb/include/tbb/task_arena.h:281: undefined reference to
>>> `tbb::interface7::internal::task_arena_base::internal_terminate()'
>>> ../../lib/librelion_lib.a(ml_optimiser_mpi.cpp.o): In function `tbb::interface7::task_arena::initialize()':
>>> /usr/local/intel/compilers_and_libraries_2019.4.243/linux/tbb/include/tbb/task_arena.h:250: undefined reference to
>>> `tbb::interface7::internal::task_arena_base::internal_initialize()'
>>> ../../lib/librelion_lib.a(ml_optimiser.cpp.o): In function
>>> `tbb::interface9::global_control::global_control(tbb::interface9::global_control::parameter, unsigned long)':
>>> /usr/local/intel/compilers_and_libraries_2019.4.243/linux/tbb/include/tbb/global_control.h:46: undefined reference to
>>> `tbb::interface9::global_control::internal_create()'
>>> ../../lib/librelion_lib.a(ml_optimiser.cpp.o): In function `tbb::interface9::global_control::~global_control()':
>>> /usr/local/intel/compilers_and_libraries_2019.4.243/linux/tbb/include/tbb/global_control.h:56: undefined reference to
>>> `tbb::interface9::global_control::internal_destroy()'
>>> /usr/local/intel/compilers_and_libraries_2019.4.243/linux/tbb/include/tbb/global_control.h:56: undefined reference to
>>> `tbb::interface9::global_control::internal_destroy()'
>>> make[2]: *** [bin/relion_refine_mpi] Error 1
>>> make[1]: *** [src/apps/CMakeFiles/refine_mpi.dir/all] Error 2
>>> make: *** [all] Error 2
>>>
>>> David
>
########################################################################
To unsubscribe from the CCPEM list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1
This message was issued to members of www.jiscmail.ac.uk/CCPEM, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
|