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Error in installation
Date: 2018/05/21 01:20
Name: M.S

Hello dear OpenMX Community.
I'm trying to install openmx in ubuntu linux distribution.
I am using Gfortan (I have ifort installed on my PC too, but after several errors, I've switched to gfortan) for fortran compiler.
also I have mkl package installed on my PC. it was installed alongside the ifort.

in makefile, I've followed the instruction on the manual, and made the following changes:

"
FFTROOT=opt/fftw3
MKLROOT=opt/intel/mkl

CC=mpicc -O3 -fopenmp -I/$(FFTROOT)/include -I/$(MKLROOT)/include
FC=-mpif90 -O3 -I/$(MKLROOT)/include
LIB= -L/$(FFTROOT)/lib -lfftw3 -L/$(MKLROOT)/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lgfortran
"




it seems ok. I've checked the dirs and the files and libs were in there. but the following error jump up when I try compile make file using "make" command. can you help me fix this problem?
ps: also there are some warning like " warning: inline function ‘Spherical_Bessel’ declared but never defined" before the error while compiling. should I worry about them?
ps2:the errors seems to have some problems with parallel openmi.just as an extra information, I've just sudo apt-get installed them using the following commands:
sudo apt-get install libibnetdisc-dev
sudo apt-get install openmpi-bin
sudo apt-get install openmpi-doc
sudo apt-get install libopenmpi-dev
+
sudo apt-get install mpich



"
elpa1.o: In function `__elpa1_MOD_solve_tridi_single':
elpa1.f90:(.text+0x140): undefined reference to `mpi_abort_'
elpa1.o: In function `transform_columns.5276':
elpa1.f90:(.text+0x360): undefined reference to `mpi_sendrecv_'
elpa1.f90:(.text+0x43e): undefined reference to `mpi_sendrecv_'
elpa1.o: In function `resort_ev.5281':
elpa1.f90:(.text+0x77d): undefined reference to `mpi_send_'
elpa1.f90:(.text+0x82b): undefined reference to `mpi_recv_'
elpa1.o: In function `global_gather.5271':
elpa1.f90:(.text+0xbaa): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0xd64): undefined reference to `mpi_sendrecv_replace_'
elpa1.f90:(.text+0xdf2): undefined reference to `mpi_allreduce_'
elpa1.o: In function `check_monotony.5257':
elpa1.f90:(.text+0xf44): undefined reference to `mpi_abort_'
elpa1.o: In function `__elpa1_MOD_merge_systems':
elpa1.f90:(.text+0x11b1): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x11ca): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x11e3): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x11fc): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x3367): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x349b): undefined reference to `mpi_recv_'
elpa1.f90:(.text+0x35fb): undefined reference to `mpi_send_'
elpa1.f90:(.text+0x506d): undefined reference to `mpi_sendrecv_replace_'
elpa1.f90:(.text+0x54d4): undefined reference to `mpi_send_'
elpa1.f90:(.text+0x551a): undefined reference to `mpi_recv_'
elpa1.f90:(.text+0x559f): undefined reference to `mpi_allreduce_'
elpa1.o: In function `merge_recursive.6557':
elpa1.f90:(.text+0x5824): undefined reference to `mpi_send_'
elpa1.f90:(.text+0x5955): undefined reference to `mpi_recv_'
elpa1.f90:(.text+0x59e0): undefined reference to `mpi_send_'
elpa1.f90:(.text+0x5b0c): undefined reference to `mpi_abort_'
elpa1.f90:(.text+0x5b5f): undefined reference to `mpi_recv_'
elpa1.o: In function `__elpa1_MOD_invert_trm_complex':
elpa1.f90:(.text+0x5fa1): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x5fb6): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x5fcb): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x5fe0): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x6584): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0x6683): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0x67b8): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0x6fb0): undefined reference to `mpi_abort_'
elpa1.o: In function `__elpa1_MOD_invert_trm_real':
elpa1.f90:(.text+0x7091): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x70a6): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x70bb): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x70d0): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x7684): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0x7781): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0x78b8): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0x80b1): undefined reference to `mpi_abort_'
elpa1.o: In function `__elpa1_MOD_solve_tridi':
elpa1.f90:(.text+0x8270): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x828a): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x82a3): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x82bc): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x853e): undefined reference to `mpi_abort_'
elpa1.f90:(.text+0x86c3): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x86d8): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x8dcc): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0x8e6d): undefined reference to `mpi_bcast_'
elpa1.o: In function `__elpa1_MOD_mult_ah_b_complex':
elpa1.f90:(.text+0x9f7c): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x9f91): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x9fae): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x9fc3): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0xa52f): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0xab75): undefined reference to `mpi_reduce_'
elpa1.f90:(.text+0xacc8): undefined reference to `mpi_reduce_'
elpa1.f90:(.text+0xae7d): undefined reference to `mpi_reduce_'
elpa1.o: In function `__elpa1_MOD_trans_ev_complex':
elpa1.f90:(.text+0xb01b): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0xb030): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0xb045): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0xb05a): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0xb6b6): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0xb9d0): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0xbe0a): undefined reference to `mpi_allreduce_'
elpa1.o: In function `__elpa1_MOD_mult_at_b_real':
elpa1.f90:(.text+0xc14f): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0xc164): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0xc181): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0xc196): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0xc6ff): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0xcd3c): undefined reference to `mpi_reduce_'
elpa1.f90:(.text+0xce98): undefined reference to `mpi_reduce_'
elpa1.f90:(.text+0xd04d): undefined reference to `mpi_reduce_'
elpa1.o: In function `__elpa1_MOD_trans_ev_real':
elpa1.f90:(.text+0xd1df): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0xd1f4): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0xd209): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0xd21e): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0xd7cc): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0xdad0): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0xdedd): undefined reference to `mpi_allreduce_'
elpa1.o: In function `elpa_transpose_vectors_':
elpa1.f90:(.text+0xe1ad): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0xe1c2): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0xe1d7): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0xe1ec): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0xe3ba): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0xe6f3): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0xe72a): undefined reference to `mpi_bcast_'
elpa1.o: In function `__elpa1_MOD_cholesky_complex':
elpa1.f90:(.text+0xe7bd): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0xe7d2): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0xe7e7): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0xe7fc): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0xef32): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0xf450): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0xf7f8): undefined reference to `mpi_abort_'
elpa1.f90:(.text+0xf8e4): undefined reference to `mpi_abort_'
elpa1.o: In function `__elpa1_MOD_cholesky_real':
elpa1.f90:(.text+0xf9c9): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0xf9de): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0xf9f3): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0xfa08): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x10111): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0x105d7): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0x10966): undefined reference to `mpi_abort_'
elpa1.f90:(.text+0x10a53): undefined reference to `mpi_abort_'
elpa1.o: In function `elpa_reduce_add_vectors_':
elpa1.f90:(.text+0x10b48): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x10b5d): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x10b72): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x10b87): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x110f7): undefined reference to `mpi_reduce_'
elpa1.o: In function `__elpa1_MOD_tridiag_complex':
elpa1.f90:(.text+0x111b3): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x111c8): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x111dd): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x111f2): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x118c5): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0x11aa2): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x11c08): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x12ad4): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x13092): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0x131d1): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x1324a): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x132b7): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x13330): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x134a6): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0x135e6): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x136cc): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x13737): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x13763): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x1379c): undefined reference to `mpi_allreduce_'
elpa1.o: In function `__elpa1_MOD_tridiag_real':
elpa1.f90:(.text+0x13a83): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x13a98): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x13aad): undefined reference to `mpi_comm_rank_'
elpa1.f90:(.text+0x13ac2): undefined reference to `mpi_comm_size_'
elpa1.f90:(.text+0x14110): undefined reference to `mpi_bcast_'
elpa1.f90:(.text+0x142a0): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x14398): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x14993): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x14a0f): undefined reference to `mpi_allreduce_'
elpa1.f90:(.text+0x14a7f): undefined reference to `mpi_allreduce_'
elpa1.o:elpa1.f90:(.text+0x14afb): more undefined references to `mpi_allreduce_' follow
solve_evp_real.o: In function `solve_evp_real_':
solve_evp_real.f90:(.text+0x67): undefined reference to `mpi_comm_rank_'
solve_evp_real.f90:(.text+0x7c): undefined reference to `mpi_comm_rank_'
solve_evp_real.f90:(.text+0xba): undefined reference to `mpi_wtime_'
solve_evp_real.f90:(.text+0xf1): undefined reference to `mpi_wtime_'
solve_evp_real.f90:(.text+0x131): undefined reference to `mpi_wtime_'
solve_evp_real.f90:(.text+0x16a): undefined reference to `mpi_wtime_'
solve_evp_real.f90:(.text+0x1a1): undefined reference to `mpi_wtime_'
solve_evp_real.o:solve_evp_real.f90:(.text+0x1da): more undefined references to `mpi_wtime_' follow
solve_evp_complex.o: In function `solve_evp_complex_':
solve_evp_complex.f90:(.text+0x8c): undefined reference to `mpi_comm_rank_'
solve_evp_complex.f90:(.text+0xae): undefined reference to `mpi_comm_size_'
solve_evp_complex.f90:(.text+0xcb): undefined reference to `mpi_comm_rank_'
solve_evp_complex.f90:(.text+0xdd): undefined reference to `mpi_comm_size_'
solve_evp_complex.f90:(.text+0x1f4): undefined reference to `mpi_wtime_'
solve_evp_complex.f90:(.text+0x230): undefined reference to `mpi_wtime_'
solve_evp_complex.f90:(.text+0x25d): undefined reference to `mpi_wtime_'
solve_evp_complex.f90:(.text+0x29b): undefined reference to `mpi_wtime_'
solve_evp_complex.f90:(.text+0x2c6): undefined reference to `mpi_wtime_'
solve_evp_complex.o:solve_evp_complex.f90:(.text+0x380): more undefined references to `mpi_wtime_' follow
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_ok_to_fork'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_single'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_ordered'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_barrier'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_4'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_reduce_nowait'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_critical'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_cmplx8_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float4_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_serialized_parallel'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_critical'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `ompc_set_nested'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_8u'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_4'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float8_max'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_push_num_threads'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_reduce_nowait'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_4'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_serialized_parallel'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_flush'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_single'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float8_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float4_max'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_master'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_4'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_global_thread_num'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_ordered'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_fork_call'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_fixed8_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_fini'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_master'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_cmplx4_add'
collect2: error: ld returned 1 exit status
makefile:260: recipe for target 'openmx' failed
make: *** [openmx] Error 1
"
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Page: [1]

Re: Error in installation ( No.1 )
Date: 2018/05/21 01:25
Name: Naoya Yamaguchi

Hi,

In my experience, this linkage problem may be solved by specifying appropriate libraries.
Can you try adding MPI ones (e.g. -lmpi; -lmpi_mpifh) if you use OpenMPI?

And I leave an example for "GCC+OpenMPI" for your information:

CC = mpicc-openmpi-gcc6 -fopenmp -O3
FC = mpif90-openmpi-gcc6 -fopenmp -O3
LIB = -L/opt/local/lib -lfftw3 -llapack -lblas -lmpi -lmpi_mpifh -lgfortran

I have installed OpenMX using the above on Mac, so, for example, you should read "mpicc-openmpi-gcc6" as "mpicc".

Regards,
Naoya Yamaguchi
メンテ
Re: Error in installation ( No.2 )
Date: 2018/05/21 23:41
Name: M.S

Hello dear Naoya Yamaguchi
thank you very much for your response. thanks to you I've installed it just fine on ubuntu 16 and 18 with the following lines:

CC = mpicc -fopenmp -O3
FC = mpicc -fopenmp -O3
LIB = -L/opt/local/lib -lfftw3 -llapack -lblas -lmpi -lmpi_mpifh -lgfortran
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Page: [1]

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