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Re: [lammps-users] << system stuck/reboot during LAMMPS compilation >>


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 8 Jul 2019 11:35:34 -0400



On Mon, Jul 8, 2019 at 11:21 AM I. Camps <icamps@...24...> wrote:
Hello Axel,

Thank you very much for your advice.

I followed and figure out that the error was due to Intel C++ compiler bot findiing gcc headers. Adding export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:/usr/include/x86_64-linux-gnu/c++/8 solve the problem.

that sounds like you have a broken intel compiler installation. been using intel compilers (on occasion) for many years and never needed to use such an ugly hack.


But now, at the end of make, I am facing the following errors:

[ 95%] Building C object examples/simulators/ex_test_Ar_fcc_cluster/CMakeFiles/ex_test_Ar_fcc_cluster.dir/ex_test_Ar_fcc_cluster.c.o
[ 95%] Linking C executable ex_test_Ar_fcc_cluster
ld: warning: libmpi.so.40, needed by ../../../libkim-api.so.2, may conflict with libmpi.so.12

...and this warning doesn't bother you??

again, why try to compile LAMMPS in the most complicated way with a non-standard (and apparently not properly configured) compiler? you are just asking for trouble and seem ill prepared to deal with those kind of problems.

axel.

 

[ 95%] Built target ex_test_Ar_fcc_cluster
Scanning dependencies of target ex_test_Ar_fcc_cluster_cpp
[ 96%] Building CXX object examples/simulators/ex_test_Ar_fcc_cluster_cpp/CMakeFiles/ex_test_Ar_fcc_cluster_cpp.dir/ex_test_Ar_fcc_cluster_cpp.cpp.o
remark #11074: Inlining inhibited by limit max-size
remark #11076: To get full report use -qopt-report=4 -qopt-report-phase ipo
[ 96%] Linking CXX executable ex_test_Ar_fcc_cluster_cpp
ld: warning: libmpi.so.40, needed by ../../../libkim-api.so.2, may conflict with libmpi.so.12
[ 96%] Built target ex_test_Ar_fcc_cluster_cpp
Scanning dependencies of target ex_test_Ar_fcc_cluster_fortran

[ 97%] Building Fortran object examples/simulators/ex_test_Ar_fcc_cluster_fortran/CMakeFiles/ex_test_Ar_fcc_cluster_fortran.dir/ex_test_Ar_fcc_cluster_fortran.f90.o
[ 98%] Linking Fortran executable ex_test_Ar_fcc_cluster_fortran
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpicxx.so.12: undefined reference to `MPII_Errhandler_set_cxx'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `PMPI_Aint_diff'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPIR_F_NeedInit'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPIR_F_MPI_WEIGHTS_EMPTY'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPIX_Comm_revoke'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPIX_Comm_failure_get_acked'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPII_Comm_get_attr'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPIR_F_MPI_UNWEIGHTED'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPII_Win_set_attr'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPIX_Comm_shrink'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `PMPI_Aint_add'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPI_F_ARGVS_NULL'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPIX_Comm_failure_ack'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPI_Aint_add'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPIX_Comm_agree'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpicxx.so.12: undefined reference to `MPII_Op_set_cxx'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPII_Comm_set_attr'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPI_WEIGHTS_EMPTY'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPIR_Err_create_code'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpicxx.so.12: undefined reference to `MPII_Keyval_set_proxy'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPIR_F_MPI_IN_PLACE'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPI_Aint_diff'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPII_Type_get_attr'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPII_Win_get_attr'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPII_F_FALSE'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `mpirinitf_'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPII_Grequest_set_lang_f77'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPIR_F_MPI_BOTTOM'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPII_Comm_get_attr_fort'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPI_UNWEIGHTED'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPIR_Err_return_comm'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPI_F_ERRCODES_IGNORE'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPII_Type_set_attr'
/usr/bin/ld: /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12: undefined reference to `MPII_F_TRUE'
collect2: error: ld returned 1 exit status
make[5]: *** [examples/simulators/ex_test_Ar_fcc_cluster_fortran/CMakeFiles/ex_test_Ar_fcc_cluster_fortran.dir/build.make:85: examples/simulators/ex_test_Ar_fcc_cluster_fortran/ex_test_Ar_fcc_cluster_fortran] Error 1
make[4]: *** [CMakeFiles/Makefile2:1450: examples/simulators/ex_test_Ar_fcc_cluster_fortran/CMakeFiles/ex_test_Ar_fcc_cluster_fortran.dir/all] Error 2
make[3]: *** [Makefile:141: all] Error 2
make[2]: *** [CMakeFiles/kim_build.dir/build.make:114: kim_build-prefix/src/kim_build-stamp/kim_build-build] Error 2
make[1]: *** [CMakeFiles/Makefile2:303: CMakeFiles/kim_build.dir/all] Error 2
make: *** [Makefile:130: all] Error 2


Regards,

Camps


On Sat, Jul 6, 2019 at 4:59 PM Axel Kohlmeyer <akohlmey@...24...> wrote:


On Sat, Jul 6, 2019 at 11:23 AM I. Camps <icamps@...24...> wrote:
Hello,

I am newbie to LAMMPS.
During the LAMMPS compilations, I did not receive any error message but my computer get stuck and then reboot.

My box configuration is a Dell G3 laptop with:
- GPU Nvidia GTX1050Ti
- Intel CPU with 12 cores
- Intel compilers (with MPI and MKL libraries)
- CUDA libraries installed
- Ubuntu 19.04

Basically, I followed the instructions on https://lammps.sandia.gov/doc/Manual.html:
1- I cloned the Git repository (firs for the unstable and then also for stable release)
2- Tried to build using the CMAKE recommendations in https://github.com/lammps/lammps/blob/master/cmake/README.md
2.1 In this case I used a modified "all_on.cmake" preset (I only removed the USER-ADIOS package)
3- Tried to compile using:

cmake -D CMAKE_C_COMPILER=mpiicc -D CMAKE_CXX_COMPILER=mpiicpc -D CMAKE_Fortran_COMPILER=mpifort -C ../cmake/presets/all_on-camps.cmake -D PKG_GPU=on GPU_API=cuda GPU_ARCH=sm_60 MKL_INCLUDE_DIRS=/opt/intel/mkl/include MKL_LIBRARIES=/opt/intel/mkl/lib/intel64 FFTW3_INCLUDE_DIRS=/opt/intel/mkl/include/fftw FFTW3_LIBRARIES=/opt/intel/compilers_and_libraries_2019.0.117/linux/mkl/interfaces/fftw3xf BUILD_MPI=on BUILD_OMP=off ../cmake

wouldn't it be smarter to start compiling with default settings and no additional packages enabled first?
... and then gradually enable packages and/or other settings/compilers?
that way you get to see more clearly at what step things go south.

axel.


 

Then my PC get stuck with the output from this command, only showing the message:

loading initial cache file ../cmake/presets/all_on-camps.cmake
-- The CXX compiler identification is Intel 19.0.0.20180804
-- Check for working CXX compiler: /opt/intel/compilers_and_libraries_2019.0.117/linux/mpi/intel64/bin/mpiicpc
-- Check for working CXX compiler: /opt/intel/compilers_and_libraries_2019.0.117/linux/mpi/intel64/bin/mpiicpc -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Git: /usr/bin/git (found version "2.20.1")
-- Running check for auto-generated files from make-based build system

Looking for the running process, I got more than 250 cmake' processes related to mpiicpc.
I did no identify any error in the CMakeOutput.log (attached here)

I really appreciate any ideas/help.

Regards,

Camps
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--
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.


--
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.