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Re: [lammps-users] Using KOKKOS package (Cuda, OpenMP ) with intel compiler.
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Re: [lammps-users] Using KOKKOS package (Cuda, OpenMP ) with intel compiler.


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Thu, 12 Oct 2017 14:45:48 -0400

you still have not provided us with the exact LAMMPS version that you are trying to compile.

your errors indicate that your system/compiler/mpi setup may be broken. or you are using a too old LAMMPS version, where there was a problem with the KOKKOS build system.

your makefile is not significantly different from the stock KOKKOS/CUDA/MPI makefile, so that can be ruled out as a source of error. i have been able to compile the 11Aug2017 stable release as well as all subsequent patch releases on our HPC cluster with openmpi 2.1.1, gcc 4.8, cuda 8 and cuda 9 without a hitch. i've also been able to use cuda 8 with gcc 5.x and cuda 9 with gcc 5.x and 6.x

axel.

On Thu, Oct 12, 2017 at 2:09 PM, A. M.M <alaa.murar@...24...> wrote:
بسم الله الرحمن الرحيم

Hello,

also i got an errors when i use mpiicpc compiler -  in the final step (linking step) -  like:

/usr/include/c++/5/bits/char_traits.h:290: undefined reference to `_intel_fast_memcpy'
/usr/include/c++/5/bits/stl_algobase.h:770: undefined reference to `_intel_fast_memset'

and more ...

now i have errors with both compilers ...

please i need some help to compile lammps with kokkos.

Thanks a lot.

On Thu, Oct 12, 2017 at 1:38 AM, A. M.M <alaa.murar@...24...> wrote:
بسم الله الرحمن الرحيم

Hello Dr. Kohlmeyer,

I am very sorry to ask questions that are always meaningless and for urgency.

I have intel compiler 17.0, cuda 9.0, gcc 5.4, and openmpi 1.10.

I attached to you the makefile that I used, but i got an errors which are

g++: error: unrecognized command line option ‘-arch=sm_30’
g++: error: unrecognized command line option ‘-Xcompiler’

and if replace mpicxx compiler with mpiicpc the errors disappears but i got a lot of warnings like:

../../lib/kokkos/core/src/Cuda/Kokkos_Cuda_UniqueToken.hpp(76): warning: __device__ annotation on a defaulted function("UniqueToken") is ignored
../dihedral_spherical.cpp:759:63: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]

and more of them ( they are differnet ), are they normal or not ?

another question:

does the skin of neighbour cmd. increase the cutoff for all pairs that i used, in other words if i need the cutoff for some pairs to be 21.0 and 17.0 and the skin to be 3.0 ( all in angstrom ) then i must put in pairs cmd. 18.0 and 14.0 ?

Thanks a lot for your patience and i am sorry again.

Thank you.

On Wed, Oct 11, 2017 at 1:04 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Tue, Oct 10, 2017 at 5:44 PM, A. M.M <alaa.murar@...1125.....> wrote:
بسم الله الرحمن الرحيم

Hello,

I am still waiting for a reply.

​please understand, that posting to this mailing list does not entitle you to get a response and part​icularly not on short notice.
there have only been 7 hours since your original post. 
this mailing list is a voluntary effort, which means that people may choose to not respond if:
- they don't have had time
- they don't understand what you are asking
- they don't know a good response
- they think, you should just follow the instructions in the manual
- they think, you should try out what your can figure out yourself and then report back with the details and errors, if any.
- they think, what you are asking for makes no sense
- they don't care

a typical rule of thumb for mailing lists is to give people at least two business days time to respond (keeping in mind that people may be located in different time zones and may have different holidays than you), before re-posting.

since the LAMMPS manual is quite detailed (sometimes too detailed), you can use that time to do some research there and perhaps it will lead you to the result you are looking for without having to repost your question.


...and after giving you a lecture on mailing list etiquette i have two comments:
- how to do what you want should be possible to figure out by carefully studying the documentation and readme files
- i don't see the point of using the intel compiler in this setup. you just make your life needlessly complicated. unlike with fortran, gcc is quite competitive and occasionally ahead of , and since you cannot use KOKKOS and USER-INTEL (the latter of which benefits a lot from using the intel compiler) at the same time, there really is not much of a reason to switch away from gcc. the performance critical part will be the GPU acceleration, anyway.

in addition to that, you don't even provide the bare minimum of useful information (LAMMPS version, intel compiler version, CUDA version, gcc version), and whether you have checked these against the list of tested/compatible combinations in the KOKKOS supporting information. in short, the better documented and detailed your inquiry, the better chances you get meaningful help (instead of getting dressed down publicly).

axel.


 

Thank you.

On Tue, Oct 10, 2017 at 5:41 PM, A. M.M <alaa.murar@...24...> wrote:
بسم الله الرحمن الرحيم

Hello,

I want to use KOKKOS package (Cuda, OpenMP) with intel compiler.

what should i do in any *-kokkos makefile to get what i want ?

Thank you.


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--
Dr. Axel Kohlmeyer  akohlmey@...36.....24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.





--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.