LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
Re: [lammps-users] Compiling LAMMPS with intel parallel studio Ubuntu 16.04
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [lammps-users] Compiling LAMMPS with intel parallel studio Ubuntu 16.04


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Tue, 22 Aug 2017 09:40:51 -0400



On Sat, Aug 19, 2017 at 4:19 PM, Afshin Arjangmehr <ms.arjangmehr@...24...> wrote:
Dear Lammps users and developers,

Recently, I tried to compile and install LAMMPS-latest release on Ubuntu 16.04 and I exactly followed the instruction given in:


I have installed intel parallel studio and I've edited my .bashrc file to include mpiiifort, mpiicc and mpiicpc as my default compilers. Also, I used the following command to compile lammps with intel Makefile:

make intel_cpu_intelmpi -j 8

but unfortunately, during final steps of compilation I face with this particular error given at the end of this email. I googled to find out what was the problem and it seems that there is a conflict between Linux default mpicxx wrapper and the one provided by intel mpicpc. In another community (GPAW), it was suggested that all the links that include mpicxx should be deleted in Makefile so this conflict never happens. But as I searched in .../Makefile & .../MAKE/OPTIONS/Makefile.intel_cpu, I couldn't find the specific lines pointing to shared libraries that cause this conflict. Can you help me solve this problem?
Also, I've succefully installed several other unix-based packages such as VASP, Quantum Espresso, Prophet and ... with my current OS, so I believe my compilers are okay.

​nevertheless the errors are clearly not coming from LAMMPS but the intel mpi library. so you have to consult the intel mpi docs for your specific version of the intel compilers for how to correctly ​link with them and adapt your makefile settings accordingly.

axel.

[...]


/opt/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_TypeGetAttr'
/opt/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPID_Datatype_direct'
/opt/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_WinSetAttr'
/opt/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPID_b_use_gettimeofday'
/opt/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_CommSetAttr'
/opt/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPID_Datatype_mem'
/opt/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_Process'
/opt/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPI_UNWEIGHTED'
/opt/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `PMPIX_Comm_reenable_anysource'
/opt/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPID_Datatype_set_contents'
/opt/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_Add_finalize'
/opt/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `PMPIX_Comm_remote_group_failed'
/opt/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_Err_return_comm'
/opt/intel//impi/5.0.1.035/intel64/lib/libmpicxx.so: undefined reference to `MPIR_Errhandler_set_cxx'
size ../lmp_intel_cpu_intelmpi
size: '../lmp_intel_cpu_intelmpi': No such file
Makefile:92: recipe for target '../lmp_intel_cpu_intelmpi' failed
make[1]: *** [../lmp_intel_cpu_intelmpi] Error 1
make[1]: Leaving directory '/home/koma/software/lammps-2017/compile/lammps-11Aug17/src/Obj_intel_cpu_intelmpi'
Makefile:158: recipe for target 'intel_cpu_intelmpi' failed
make: *** [intel_cpu_intelmpi] Error 2

Thank you very much.


--
With Best Regards
Afshin Arjhangemehr
PhD candidate in Radiation Application

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
lammps-users mailing list
lammps-users@...6297....sourceforge.net
https://lists.sourceforge.net/lists/listinfo/lammps-users




--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.